h5ad filesThe purpose of this package is to make it easy to query the Human Cell Atlas Data Portal via their data browser API. Visit the Human Cell Atlas for more information on the project.
Evaluate the following code chunk to install packages required for this vignette.
## install from Bioconductor if you haven't already
pkgs <- c("httr", "dplyr", "LoomExperiment", "hca")
pkgs_needed <- pkgs[!pkgs %in% rownames(installed.packages())]
BiocManager::install(pkgs_needed)Load the packages into your R session.
library(httr)
library(dplyr)
library(LoomExperiment)
library(hca)To illustrate use of this package, consider the task of downloading a ‘loom’ file summarizing single-cell gene expression observed in an HCA research project. This could be accomplished by visiting the HCA data portal (at https://data.humancellatlas.org/explore) in a web browser and selecting projects interactively, but it is valuable to accomplish the same goal in a reproducible, flexible, programmatic way. We will (1) discover projects available in the HCA Data Coordinating Center that have loom files; and (2) retrieve the file from the HCA and import the data into R as a ‘LoomExperiment’ object. For illustration, we focus on the ‘Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns’ project.
Use projects() to retrieve all projects in the HCA’s default catalog.
projects()
## # A tibble: 208 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 74b6d569-3b11-42ef-b… 1.3 Million… <chr [1]> <chr [1]> <chr [1]>
## 2 53c53cd4-8127-4e12-b… A Cellular … <chr [2]> <chr [1]> <chr [1]>
## 3 7027adc6-c9c9-46f3-8… A Cellular … <chr [1]> <chr [1]> <chr [1]>
## 4 60ea42e1-af49-42f5-8… A Protocol … <chr [1]> <chr [1]> <chr [1]>
## 5 ef1e3497-515e-4bbe-8… A Single-Ce… <chr [1]> <chr [3]> <chr [3]>
## 6 f86f1ab4-1fbb-4510-a… A Single-Ce… <chr [2]> <chr [1]> <chr [1]>
## 7 602628d7-c038-48a8-a… A Single-ce… <chr [1]> <chr [3]> <chr [3]>
## 8 c1810dbc-16d2-45c3-b… A cell atla… <chr [2]> <chr [2]> <chr [2]>
## 9 5116c081-8be7-49c5-8… A comprehen… <chr [1]> <chr [1]> <chr [1]>
## 10 a9301beb-e9fa-42fe-b… A human cel… <chr [1]> <chr [14]> <chr [14]>
## # … with 198 more rowsUse filters() to restrict the projects to just those that contain at
least one ‘loom’ file.
project_filter <- filters(fileFormat = list(is = "loom"))
project_tibble <- projects(project_filter)
project_tibble
## # A tibble: 78 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 53c53cd4-8127-4e12-b… A Cellular … <chr [2]> <chr [1]> <chr [1]>
## 2 7027adc6-c9c9-46f3-8… A Cellular … <chr [1]> <chr [1]> <chr [1]>
## 3 c1810dbc-16d2-45c3-b… A cell atla… <chr [2]> <chr [2]> <chr [2]>
## 4 a9301beb-e9fa-42fe-b… A human cel… <chr [1]> <chr [14]> <chr [14]>
## 5 996120f9-e84f-409f-a… A human sin… <chr [1]> <chr [1]> <chr [1]>
## 6 842605c7-375a-47c5-9… A single ce… <chr [1]> <chr [1]> <chr [1]>
## 7 a004b150-1c36-4af6-9… A single-ce… <chr [1]> <chr [1]> <chr [1]>
## 8 4a95101c-9ffc-4f30-a… A single-ce… <chr [1]> <chr [4]> <chr [4]>
## 9 1cd1f41f-f81a-486b-a… A single-ce… <chr [1]> <chr [1]> <chr [1]>
## 10 8185730f-4113-40d3-9… A single-ce… <chr [1]> <chr [1]> <chr [1]>
## # … with 68 more rowsUse standard R commands to further filter projects to the one we are
interested in, with title starting with “Single…”.
Extract the unique projectId for this project.
project_tibble %>%
filter(startsWith(projectTitle, "Single")) %>%
t()
## [,1]
## projectId "0c3b7785-f74d-4091-8616-a68757e4c2a8"
## projectTitle "Single cell RNA sequencing of multiple myeloma II"
## genusSpecies "Homo sapiens"
## samples.organ "hematopoietic system"
## specimens.organ "hematopoietic system"
## [,2]
## projectId "7b947aa2-43a7-4082-afff-222a3e3a4635"
## projectTitle "Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids"
## genusSpecies character,2
## samples.organ "whole embryos"
## specimens.organ character,2
## [,3]
## projectId "99101928-d9b1-4aaf-b759-e97958ac7403"
## projectTitle "Single cell RNA-seq of human pancreatic endocrine cells from Juvenile, adult control and type 2 dia" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "Pancreas"
## specimens.organ "Pancreas"
## [,4]
## projectId "520afa10-f9d2-4e93-ab7a-26c4c863ce18"
## projectTitle "Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs)"
## genusSpecies "Homo sapiens"
## samples.organ "tonsil"
## specimens.organ "tonsil"
## [,5]
## projectId "23587fb3-1a4a-4f58-ad74-cc9a4cb4c254"
## projectTitle "Single cell analysis of human fetal liver captures the transcriptional profile of hepatobiliary hyb" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "liver"
## specimens.organ "liver"
## [,6]
## projectId "116965f3-f094-4769-9d28-ae675c1b569c"
## projectTitle "Single cell profiling of human induced dendritic cells generated by direct reprogramming of embryon" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "embryo"
## specimens.organ "embryo"
## [,7]
## projectId "f6133d2a-9f3d-4ef9-9c19-c23d6c7e6cc0"
## projectTitle "Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypox" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ character,0
## specimens.organ "breast"
## [,8]
## projectId "cddab57b-6868-4be4-806f-395ed9dd635a"
## projectTitle "Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging an" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "pancreas"
## specimens.organ "pancreas"
## [,9]
## projectId "2d846095-8a33-4f3c-97d4-585bafac13b4"
## projectTitle "Single-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of huma" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "brain"
## specimens.organ "brain"
## [,10]
## projectId "e8808cc8-4ca0-4096-80f2-bba73600cba6"
## projectTitle "Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated" [truncated]
## genusSpecies "Mus musculus"
## samples.organ character,3
## specimens.organ character,3
## [,11]
## projectId "b51f49b4-0d2e-4cbd-bbd5-04cd171fc2fa"
## projectTitle "Single-cell RNA Sequencing of human microglia from post mortem Alzheimers Disease CNS tissue."
## genusSpecies "Homo sapiens"
## samples.organ "brain"
## specimens.organ "brain"
## [,12]
## projectId "2ef3655a-973d-4d69-9b41-21fa4041eed7"
## projectTitle "Single-cell RNA sequencing of normal human kidney"
## genusSpecies "Homo sapiens"
## samples.organ "kidney"
## specimens.organ "kidney"
## [,13]
## projectId "559bb888-7829-41f2-ace5-2c05c7eb81e9"
## projectTitle "Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human."
## genusSpecies "Homo sapiens"
## samples.organ character,3
## specimens.organ character,3
## [,14]
## projectId "4bec484d-ca7a-47b4-8d48-8830e06ad6db"
## projectTitle "Single-cell RNA-Seq Investigation of Foveal and Peripheral Expression in the Human Retina"
## genusSpecies "Homo sapiens"
## samples.organ "retina"
## specimens.organ "retina"
## [,15]
## projectId "2043c65a-1cf8-4828-a656-9e247d4e64f1"
## projectTitle "Single-cell RNA-seq analysis throughout a 125-day differentiation protocol that converted H1 human" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ character,0
## specimens.organ "embryo"
## [,16]
## projectId "ae71be1d-ddd8-4feb-9bed-24c3ddb6e1ad"
## projectTitle "Single-cell RNA-seq analysis of human pancreas from healthy individuals and type 2 diabetes patient" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "pancreas"
## specimens.organ "pancreas"
## [,17]
## projectId "f48e7c39-cc67-4055-9d79-bc437892840c"
## projectTitle "Single-cell RNA-seq of human peripheral blood NKT cells"
## genusSpecies "Homo sapiens"
## samples.organ "blood"
## specimens.organ "blood"
## [,18]
## projectId "05be4f37-4506-429b-b112-506444507d62"
## projectTitle "Single-cell RNA-seq reveals heterogeneity within human pre-cDCs"
## genusSpecies "Homo sapiens"
## samples.organ "blood"
## specimens.organ "blood"
## [,19]
## projectId "c1a9a93d-d9de-4e65-9619-a9cec1052eaa"
## projectTitle "Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineage" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "lung"
## specimens.organ "lung"
## [,20]
## projectId "07073c12-8006-4710-a00b-23abdb814904"
## projectTitle "Single-cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expressio" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "blood vessel"
## specimens.organ "blood vessel"
## [,21]
## projectId "962bd805-eb89-4c54-bad2-008e497d1307"
## projectTitle "Single-cell analysis reveals congruence between kidney organoids and human fetal kidney"
## genusSpecies "Homo sapiens"
## samples.organ character,0
## specimens.organ "skin of body"
## [,22]
## projectId "1ce3b3dc-02f2-44a8-96da-d6d107b27a76"
## projectTitle "Single-cell analysis reveals the continuum of human lympho-myeloid progenitor cells"
## genusSpecies "Homo sapiens"
## samples.organ "umbilical cord"
## specimens.organ "umbilical cord"
## [,23]
## projectId "ccd1f1ba-74ce-469b-9fc9-f6faea623358"
## projectTitle "Single-cell omics reveal human mononuclear phagocyte heterogeneity and inflammatory DC in health an" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "blood"
## specimens.organ "blood"
## [,24]
## projectId "5ee710d7-e2d5-4fe2-818d-15f5e31dae32"
## projectTitle "Single-cell survey of human lymphatics unveils marked endothelial cell heterogeneity and mechanisms" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "lymph node"
## specimens.organ "lymph node"
## [,25]
## projectId "a39728aa-70a0-4201-b0a2-81b7badf3e71"
## projectTitle "Single-cell transcriptional profiles in human and mouse skeletal muscle"
## genusSpecies character,2
## samples.organ "skeletal muscle organ"
## specimens.organ "skeletal muscle organ"
## [,26]
## projectId "78b2406d-bff2-46fc-8b61-20690e602227"
## projectTitle "Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes"
## genusSpecies "Homo sapiens"
## samples.organ "pancreas"
## specimens.organ "pancreas"
## [,27]
## projectId "2a72a4e5-66b2-405a-bb7c-1e463e8febb0"
## projectTitle "Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "hematopoietic system"
## specimens.organ "hematopoietic system"
## [,28]
## projectId "24c654a5-caa5-440a-8f02-582921f2db4a"
## projectTitle "Single-cell transcriptomics uncovers human corneal limbal stem cells and their differentiation traj" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ "eye"
## specimens.organ "eye"
## [,29]
## projectId "ce7b12ba-664f-4f79-8fc7-3de6b1892183"
## projectTitle "Single-nucleus RNA sequencing of human cortex affected by multiple sclerosis."
## genusSpecies "Homo sapiens"
## samples.organ "brain"
## specimens.organ "brain"
projectIds <-
project_tibble %>%
filter(startsWith(projectTitle, "Single")) %>%
dplyr::pull(projectId)
projectId <- projectIds[1]files() retrieves (the first 1000) files from the Human Cell Atlas
data portal. Construct a filter to restrict the files to loom files
from the project we are interested in.
file_filter <- filters(
projectId = list(is = projectId),
fileFormat = list(is = "loom")
)
# only the two smallest files
file_tibble <- files(file_filter, size = 2, sort = "fileSize", order = "asc")
file_tibble
## # A tibble: 2 × 8
## fileId name fileFormat size version projectTitle projectId url
## <chr> <chr> <chr> <int> <chr> <chr> <chr> <chr>
## 1 fe214fea-cc68-56… bone… loom 4.04e7 2021-0… Single cell… 0c3b7785… http…
## 2 3014ec47-1399-57… Bone… loom 6.35e7 2021-1… Single cell… 0c3b7785… http…files_download() will download one or more files (one for each row)
in file_tibble. The download is more complicated than simply
following the url column of file_tibble, so it is not possible to
simply copy the url into a browser. We’ll download the file and then
immediately import it into R.
file_locations <- file_tibble %>% files_download()
LoomExperiment::import(unname(file_locations[1]),
type ="SingleCellLoomExperiment")
## class: SingleCellLoomExperiment
## dim: 58347 3762
## metadata(15): last_modified CreationDate ...
## project.provenance.document_id specimen_from_organism.organ
## assays(1): matrix
## rownames: NULL
## rowData names(29): Gene antisense_reads ... reads_per_molecule
## spliced_reads
## colnames: NULL
## colData names(43): CellID antisense_reads ... reads_unmapped
## spliced_reads
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowGraphs(0): NULL
## colGraphs(0): NULLNote that files_download() uses [BiocFileCache][https://bioconductor.org/packages/BiocFileCache],
so individual files are only downloaded once.
h5ad filesThis example walks through the process of file discovery and retrieval
in a little more detail, using h5ad files created by the Python
AnnData analysis software and available for some experiments in the
default catalog.
The first challenge is to understand what file formats are available from the HCA. Obtain a tibble describing the ‘facets’ of the data, the number of terms used in each facet, and the number of distinct values used to describe projects.
projects_facets()
## # A tibble: 35 × 3
## facet n_terms n_values
## <chr> <int> <int>
## 1 assayType 1 208
## 2 biologicalSex 5 332
## 3 cellLineType 6 216
## 4 contactName 1851 2276
## 5 contentDescription 38 667
## 6 developmentStage 132 416
## 7 donorDisease 181 421
## 8 effectiveOrgan 108 378
## 9 fileFormat 41 674
## 10 fileSource 10 469
## # … with 25 more rowsNote the fileFormat facet, and repeat projects_facets() to
discover detail about available file formats
projects_facets("fileFormat")
## # A tibble: 41 × 3
## facet term count
## <chr> <chr> <int>
## 1 fileFormat fastq.gz 173
## 2 fileFormat loom 78
## 3 fileFormat bam 77
## 4 fileFormat tar 45
## 5 fileFormat tsv.gz 35
## 6 fileFormat mtx.gz 30
## 7 fileFormat txt.gz 30
## 8 fileFormat bai 26
## 9 fileFormat csv 26
## 10 fileFormat csv.gz 20
## # … with 31 more rowsNote that there are 8 uses of the h5ad file format. Use this as a
filter to discover relevant projects.
filters <- filters(fileFormat = list(is = "h5ad"))
projects(filters)
## # A tibble: 13 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 c1810dbc-16d2-45c3-b… A cell atla… <chr [2]> <chr [2]> <chr [2]>
## 2 1dddae6e-3753-48af-b… Cell Types … <chr [1]> <chr [1]> <chr [2]>
## 3 ad98d3cd-26fb-4ee3-9… Cells of th… <chr [1]> <chr [1]> <chr [1]>
## 4 83f5188e-3bf7-4956-9… Distinct mi… <chr [1]> <chr [2]> <chr [2]>
## 5 2f676143-80c2-4bc6-b… Integrative… <chr [1]> <chr [1]> <chr [1]>
## 6 c4077b3c-5c98-4d26-a… Ischaemic s… <chr [1]> <chr [3]> <chr [3]>
## 7 091cf39b-01bc-42e5-9… Profiling o… <chr [1]> <chr [0]> <chr [1]>
## 8 f83165c5-e2ea-4d15-a… Reconstruct… <chr [1]> <chr [3]> <chr [3]>
## 9 31887183-a72c-4308-9… Single-nucl… <chr [1]> <chr [7]> <chr [7]>
## 10 abe1a013-af7a-45ed-8… Spatio-temp… <chr [1]> <chr [1]> <chr [1]>
## 11 b963bd4b-4bc1-4404-8… The cellula… <chr [1]> <chr [1]> <chr [1]>
## 12 4e6f083b-5b9a-4393-9… The emergen… <chr [1]> <chr [3]> <chr [3]>
## 13 455b46e6-d8ea-4611-8… Transcripto… <chr [1]> <chr [3]> <chr [3]>The default tibble produced by projects() contains only some of the
information available; the information is much richer.
To obtain a tibble with an expanded set of columns, you can specify that using
the as parameter set to "tibble_expanded".
# an expanded set of columns for all or the first 4 projects
projects(as = 'tibble_expanded', size = 4)
## # A tibble: 4 × 102
## projectId cellSuspensions… cellSuspensions… cellSuspensions… cellSuspensions…
## <chr> <list> <chr> <list> <int>
## 1 74b6d569-… <chr [1]> brain <chr [1]> 1330000
## 2 53c53cd4-… <chr [2]> prostate gland <chr [7]> 108701
## 3 7027adc6-… <chr [0]> heart <chr [0]> NA
## 4 60ea42e1-… <chr [1]> oral cavity <chr [1]> 1145
## # … with 97 more variables: dates.aggregateLastModifiedDate <chr>,
## # dates.aggregateSubmissionDate <chr>, dates.aggregateUpdateDate <chr>,
## # dates.lastModifiedDate <chr>, dates.submissionDate <chr>,
## # dates.updateDate <chr>, donorOrganisms.biologicalSex <chr>,
## # donorOrganisms.developmentStage <list>, donorOrganisms.disease <chr>,
## # donorOrganisms.donorCount <int>, donorOrganisms.genusSpecies <list>,
## # donorOrganisms.id <list>, donorOrganisms.organismAgeRange.gte <list>, …In the next sections, we’ll cover other options for the as parameter, and the data formats
they return.
projects() as an R listInstead of retrieving the result of projects() as a tibble, retrieve
it as a ‘list-of-lists’
projects_list <- projects(as = "list")This is a complicated structure. We will use lengths(), names(),
and standard R list selection operations to navigate this a bit. At
the top level there are three elements.
lengths(projects_list)
## hits pagination termFacets
## 208 8 36hits represents each project as a list, e.g,.
lengths(projects_list$hits[[1]])
## protocols entryId sources projects
## 2 1 1 1
## samples specimens cellLines donorOrganisms
## 1 1 0 1
## organoids cellSuspensions dates fileTypeSummaries
## 0 1 1 2shows that there are 10 different ways in which the first project is described. Each component is itself a list-of-lists, e.g.,
lengths(projects_list$hits[[1]]$projects[[1]])
## projectId projectTitle projectShortname laboratory
## 1 1 1 1
## estimatedCellCount projectDescription contributors publications
## 1 1 6 1
## supplementaryLinks matrices contributedAnalyses accessions
## 1 0 1 3
## accessible
## 1
projects_list$hits[[1]]$projects[[1]]$projectTitle
## [1] "1.3 Million Brain Cells from E18 Mice"One can use standard R commands to navigate this data structure, and
to, e.g., extract the projectTitle of each project.
projects() as an lolUse as = "lol" to create a more convenient way to select, filter and
extract elements from the list-of-lists by projects().
lol <- projects(as = "lol")
lol
## # class: lol_hca lol
## # number of distinct paths: 11480
## # total number of elements: 112959
## # number of leaf paths: 8482
## # number of leaf elements: 83771
## # lol_path():
## # A tibble: 11,480 × 3
## path n is_leaf
## <chr> <int> <lgl>
## 1 hits 1 FALSE
## 2 hits[*] 208 FALSE
## 3 hits[*].cellLines 208 FALSE
## 4 hits[*].cellLines[*] 33 FALSE
## 5 hits[*].cellLines[*].cellLineType 33 FALSE
## 6 hits[*].cellLines[*].cellLineType[*] 41 TRUE
## 7 hits[*].cellLines[*].id 33 FALSE
## 8 hits[*].cellLines[*].id[*] 236 TRUE
## 9 hits[*].cellLines[*].modelOrgan 33 FALSE
## 10 hits[*].cellLines[*].modelOrgan[*] 41 TRUE
## # … with 11,470 more rowsUse lol_select() to restrict the lol to particular paths, and
lol_filter() to filter results to paths that are leafs, or with
specific numbers of entries.
lol_select(lol, "hits[*].projects[*]")
## # class: lol_hca lol
## # number of distinct paths: 11357
## # total number of elements: 65249
## # number of leaf paths: 8424
## # number of leaf elements: 51661
## # lol_path():
## # A tibble: 11,357 × 3
## path n is_leaf
## <chr> <int> <lgl>
## 1 hits[*].projects[*] 208 FALSE
## 2 hits[*].projects[*].accessible 208 TRUE
## 3 hits[*].projects[*].accessions 208 FALSE
## 4 hits[*].projects[*].accessions[*] 547 FALSE
## 5 hits[*].projects[*].accessions[*].accession 547 TRUE
## 6 hits[*].projects[*].accessions[*].namespace 547 TRUE
## 7 hits[*].projects[*].contributedAnalyses 208 FALSE
## 8 hits[*].projects[*].contributedAnalyses.developmentStage 4 FALSE
## 9 hits[*].projects[*].contributedAnalyses.developmentStage.adult 4 FALSE
## 10 hits[*].projects[*].contributedAnalyses.developmentStage.adult… 2 FALSE
## # … with 11,347 more rows
lol_select(lol, "hits[*].projects[*]") |>
lol_filter(n == 44, is_leaf)
## # class: lol_hca lol
## # number of distinct paths: 0
## # total number of elements: 0
## # number of leaf paths: 0
## # number of leaf elements: 0
## # lol_path():
## # A tibble: 0 × 3
## # … with 3 variables: path <chr>, n <int>, is_leaf <lgl>lol_pull() extracts a path from the lol as a vector; lol_lpull()
extracts paths as lists.
titles <- lol_pull(lol, "hits[*].projects[*].projectTitle")
length(titles)
## [1] 208
head(titles, 2)
## [1] "1.3 Million Brain Cells from E18 Mice"
## [2] "A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra"projects() tibbles with specific columnsThe path or its abbreviation can be used to specify the columns of
the tibble to be returned by the projects() query.
Here we retrieve additional details of donor count and total cells by adding appropriate path abbreviations to a named character vector. Names on the character vector can be used to rename the path more concisely, but the paths must uniquely identify elements in the list-of-lists.
columns <- c(
projectId = "hits[*].entryId",
projectTitle = "hits[*].projects[*].projectTitle",
genusSpecies = "hits[*].donorOrganisms[*].genusSpecies[*]",
donorCount = "hits[*].donorOrganisms[*].donorCount",
cellSuspensions.organ = "hits[*].cellSuspensions[*].organ[*]",
totalCells = "hits[*].cellSuspensions[*].totalCells"
)
projects <- projects(filters, columns = columns)
projects
## # A tibble: 13 × 6
## projectId projectTitle genusSpecies donorCount cellSuspensions… totalCells
## <chr> <chr> <list> <int> <list> <list>
## 1 c1810dbc-16… A cell atla… <chr [2]> 24 <chr [2]> <int [2]>
## 2 1dddae6e-37… Cell Types … <chr [1]> 6 <chr [1]> <int [0]>
## 3 ad98d3cd-26… Cells of th… <chr [1]> 14 <chr [1]> <int [1]>
## 4 83f5188e-3b… Distinct mi… <chr [1]> 6 <chr [2]> <int [2]>
## 5 2f676143-80… Integrative… <chr [1]> 15 <chr [1]> <int [0]>
## 6 c4077b3c-5c… Ischaemic s… <chr [1]> 14 <chr [3]> <int [3]>
## 7 091cf39b-01… Profiling o… <chr [1]> 3 <chr [1]> <int [1]>
## 8 f83165c5-e2… Reconstruct… <chr [1]> 16 <chr [3]> <int [0]>
## 9 31887183-a7… Single-nucl… <chr [1]> 16 <chr [7]> <int [0]>
## 10 abe1a013-af… Spatio-temp… <chr [1]> 8 <chr [1]> <int [0]>
## 11 b963bd4b-4b… The cellula… <chr [1]> 120 <chr [1]> <int [1]>
## 12 4e6f083b-5b… The emergen… <chr [1]> 6 <chr [3]> <int [3]>
## 13 455b46e6-d8… Transcripto… <chr [1]> 4 <chr [3]> <int [3]>Note that the cellSuspensions.organ and totalCells columns have more than
one entry per project.
projects |>
select(projectId, cellSuspensions.organ, totalCells)
## # A tibble: 13 × 3
## projectId cellSuspensions.organ totalCells
## <chr> <list> <list>
## 1 c1810dbc-16d2-45c3-b45e-3e675f88d87b <chr [2]> <int [2]>
## 2 1dddae6e-3753-48af-b20e-fa22abad125d <chr [1]> <int [0]>
## 3 ad98d3cd-26fb-4ee3-99c9-8a2ab085e737 <chr [1]> <int [1]>
## 4 83f5188e-3bf7-4956-9544-cea4f8997756 <chr [2]> <int [2]>
## 5 2f676143-80c2-4bc6-b7b4-2613fe0fadf0 <chr [1]> <int [0]>
## 6 c4077b3c-5c98-4d26-a614-246d12c2e5d7 <chr [3]> <int [3]>
## 7 091cf39b-01bc-42e5-9437-f419a66c8a45 <chr [1]> <int [1]>
## 8 f83165c5-e2ea-4d15-a5cf-33f3550bffde <chr [3]> <int [0]>
## 9 31887183-a72c-4308-9eac-c6140313f39c <chr [7]> <int [0]>
## 10 abe1a013-af7a-45ed-8c26-f3793c24a1f4 <chr [1]> <int [0]>
## 11 b963bd4b-4bc1-4404-8425-69d74bc636b8 <chr [1]> <int [1]>
## 12 4e6f083b-5b9a-4393-9890-2a83da8188f1 <chr [3]> <int [3]>
## 13 455b46e6-d8ea-4611-861e-de720a562ada <chr [3]> <int [3]>In this case, the mapping between cellSuspensions.organ and totalCells
is clear, but in general more refined navigation of the lol structure may be
necessary.
projects |>
select(projectId, cellSuspensions.organ, totalCells) |>
filter(lengths(totalCells) > 0) |>
tidyr::unnest(c("cellSuspensions.organ", "totalCells"))
## # A tibble: 16 × 3
## projectId cellSuspensions.organ totalCells
## <chr> <chr> <int>
## 1 c1810dbc-16d2-45c3-b45e-3e675f88d87b thymus 456000
## 2 c1810dbc-16d2-45c3-b45e-3e675f88d87b colon 16000
## 3 ad98d3cd-26fb-4ee3-99c9-8a2ab085e737 heart 791000
## 4 83f5188e-3bf7-4956-9544-cea4f8997756 immune organ 381
## 5 83f5188e-3bf7-4956-9544-cea4f8997756 large intestine 1141
## 6 c4077b3c-5c98-4d26-a614-246d12c2e5d7 esophagus 93267
## 7 c4077b3c-5c98-4d26-a614-246d12c2e5d7 spleen 66553
## 8 c4077b3c-5c98-4d26-a614-246d12c2e5d7 lung 40025
## 9 091cf39b-01bc-42e5-9437-f419a66c8a45 hematopoietic system 1480000
## 10 b963bd4b-4bc1-4404-8425-69d74bc636b8 blood 800000
## 11 4e6f083b-5b9a-4393-9890-2a83da8188f1 embryo 27083
## 12 4e6f083b-5b9a-4393-9890-2a83da8188f1 endoderm 54166
## 13 4e6f083b-5b9a-4393-9890-2a83da8188f1 presumptive gut 30952
## 14 455b46e6-d8ea-4611-861e-de720a562ada bone marrow 87532
## 15 455b46e6-d8ea-4611-861e-de720a562ada spleen 60043
## 16 455b46e6-d8ea-4611-861e-de720a562ada blood 25016Select the following entry, augment the filter, and query available files
projects %>%
filter(startsWith(projectTitle, "Reconstruct")) %>%
t()
## [,1]
## projectId "f83165c5-e2ea-4d15-a5cf-33f3550bffde"
## projectTitle "Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics"
## genusSpecies "Homo sapiens"
## donorCount 16
## cellSuspensions.organ character,3
## totalCells integer,0This approach can be used to customize the tibbles returned by the
other main functions in the package, files(), samples(), and
bundles().
The relevant file can be selected and downloaded using the technique in the first example.
filters <- filters(
projectId = list(is = "f83165c5-e2ea-4d15-a5cf-33f3550bffde"),
fileFormat = list(is = "h5ad")
)
files <-
files(filters) %>%
head(1) # only first file, for demonstration
files %>% t()
## [,1]
## fileId "6d4fedcf-857d-5fbb-9928-8b9605500a69"
## name "vento18_ss2.processed.h5ad"
## fileFormat "h5ad"
## size "82121633"
## version "2021-02-10T16:56:40.419579Z"
## projectTitle "Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics"
## projectId "f83165c5-e2ea-4d15-a5cf-33f3550bffde"
## url "https://service.azul.data.humancellatlas.org/repository/files/6d4fedcf-857d-5fbb-9928-8b9605500a69?catalog=dcp13&version=2021-02-10T16%3A56%3A40.419579Z"file_path <- files_download(files)"h5ad" files can be read as SingleCellExperiment objects using the
zellkonverter package.
## don't want large amount of data read from disk
sce <- zellkonverter::readH5AD(file_path, use_hdf5 = TRUE)
sceproject_filter <- filters(fileFormat = list(is = "csv"))
project_tibble <- projects(project_filter)
project_tibble %>%
filter(
startsWith(
projectTitle,
"Reconstructing the human first trimester"
)
)
## # A tibble: 1 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 f83165c5-e2ea-4d15-a5… Reconstruct… <chr [1]> <chr [3]> <chr [3]>
projectId <-
project_tibble %>%
filter(
startsWith(
projectTitle,
"Reconstructing the human first trimester"
)
) %>%
pull(projectId)
file_filter <- filters(
projectId = list(is = projectId),
fileFormat = list(is = "csv")
)
## first 4 files will be returned
file_tibble <- files(file_filter, size = 4)
file_tibble %>%
files_download()
## 7f9a181e-24c5-5462-b308-7fef5b1bda2a-2021-02-10T16:56:40.419579Z
## "/home/biocbuild/.cache/R/hca/372fcc60a648de_372fcc60a648de.csv"
## d04c6e3c-b740-5586-8420-4480a1b5706c-2021-02-10T16:56:40.419579Z
## "/home/biocbuild/.cache/R/hca/372fcc22f276fe_372fcc22f276fe.csv"
## d30ffc0b-7d6e-5b85-aff9-21ec69663a81-2021-02-10T16:56:40.419579Z
## "/home/biocbuild/.cache/R/hca/372fcc2643c2b7_372fcc2643c2b7.csv"
## e1517725-01b0-5346-9788-afca63e9993a-2021-02-10T16:56:40.419579Z
## "/home/biocbuild/.cache/R/hca/372fcc758ae5_372fcc758ae5.csv"The files(), bundles(), and samples() can all return many 1000’s
of results. It is necessary to ‘page’ through these to see all of
them. We illustrate pagination with projects(), retrieving only 30 projects.
Pagination works for the default tibble output
page_1_tbl <- projects(size = 30)
page_1_tbl
## # A tibble: 30 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 74b6d569-3b11-42ef-b… 1.3 Million… <chr [1]> <chr [1]> <chr [1]>
## 2 53c53cd4-8127-4e12-b… A Cellular … <chr [2]> <chr [1]> <chr [1]>
## 3 7027adc6-c9c9-46f3-8… A Cellular … <chr [1]> <chr [1]> <chr [1]>
## 4 60ea42e1-af49-42f5-8… A Protocol … <chr [1]> <chr [1]> <chr [1]>
## 5 ef1e3497-515e-4bbe-8… A Single-Ce… <chr [1]> <chr [3]> <chr [3]>
## 6 f86f1ab4-1fbb-4510-a… A Single-Ce… <chr [2]> <chr [1]> <chr [1]>
## 7 602628d7-c038-48a8-a… A Single-ce… <chr [1]> <chr [3]> <chr [3]>
## 8 c1810dbc-16d2-45c3-b… A cell atla… <chr [2]> <chr [2]> <chr [2]>
## 9 5116c081-8be7-49c5-8… A comprehen… <chr [1]> <chr [1]> <chr [1]>
## 10 a9301beb-e9fa-42fe-b… A human cel… <chr [1]> <chr [14]> <chr [14]>
## # … with 20 more rows
page_2_tbl <- page_1_tbl %>% hca_next()
page_2_tbl
## # A tibble: 30 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 74493e98-44fc-48b0-a… CD27hiCD38h… <chr [1]> <chr [1]> <chr [1]>
## 2 7ac8822c-4ef0-4194-a… COVID-19 se… <chr [1]> <chr [1]> <chr [1]>
## 3 da2747fa-2921-42e0-a… Capturing h… <chr [1]> <chr [0]> <chr [1]>
## 4 1dddae6e-3753-48af-b… Cell Types … <chr [1]> <chr [1]> <chr [2]>
## 5 f81efc03-9f56-4354-a… Cell hashin… <chr [1]> <chr [1]> <chr [1]>
## 6 ad98d3cd-26fb-4ee3-9… Cells of th… <chr [1]> <chr [1]> <chr [1]>
## 7 21ea8ddb-525f-4f1f-a… Cellular he… <chr [1]> <chr [4]> <chr [4]>
## 8 cc95ff89-2e68-4a08-a… Census of I… <chr [1]> <chr [2]> <chr [2]>
## 9 6c040a93-8cf8-4fd5-9… Characteriz… <chr [1]> <chr [1]> <chr [1]>
## 10 2ad191cd-bd7a-409b-9… Co-evolutio… <chr [1]> <chr [1]> <chr [1]>
## # … with 20 more rows
## should be identical to page_1_tbl
page_2_tbl %>% hca_prev()
## # A tibble: 30 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 74b6d569-3b11-42ef-b… 1.3 Million… <chr [1]> <chr [1]> <chr [1]>
## 2 53c53cd4-8127-4e12-b… A Cellular … <chr [2]> <chr [1]> <chr [1]>
## 3 7027adc6-c9c9-46f3-8… A Cellular … <chr [1]> <chr [1]> <chr [1]>
## 4 60ea42e1-af49-42f5-8… A Protocol … <chr [1]> <chr [1]> <chr [1]>
## 5 ef1e3497-515e-4bbe-8… A Single-Ce… <chr [1]> <chr [3]> <chr [3]>
## 6 f86f1ab4-1fbb-4510-a… A Single-Ce… <chr [2]> <chr [1]> <chr [1]>
## 7 602628d7-c038-48a8-a… A Single-ce… <chr [1]> <chr [3]> <chr [3]>
## 8 c1810dbc-16d2-45c3-b… A cell atla… <chr [2]> <chr [2]> <chr [2]>
## 9 5116c081-8be7-49c5-8… A comprehen… <chr [1]> <chr [1]> <chr [1]>
## 10 a9301beb-e9fa-42fe-b… A human cel… <chr [1]> <chr [14]> <chr [14]>
## # … with 20 more rowsPagination also works for the lol objects
page_1_lol <- projects(size = 5, as = "lol")
page_1_lol %>%
lol_pull("hits[*].projects[*].projectTitle")
## [1] "1.3 Million Brain Cells from E18 Mice"
## [2] "A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra"
## [3] "A Cellular Atlas of Pitx2-Dependent Cardiac Development."
## [4] "A Protocol for Revealing Oral Neutrophil Heterogeneity by Single-Cell Immune Profiling in Human Saliva"
## [5] "A Single-Cell Atlas of the Human Healthy Airways."
page_2_lol <-
page_1_lol %>%
hca_next()
page_2_lol %>%
lol_pull("hits[*].projects[*].projectTitle")
## [1] "A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure"
## [2] "A Single-cell Transcriptomic Atlas of Human Intervertebral Disc"
## [3] "A cell atlas of human thymic development defines T cell repertoire formation"
## [4] "A comprehensive single cell transcriptional landscape of human hematopoietic progenitors"
## [5] "A human cell atlas of fetal gene expression."
## should be identical to page_1_lol
page_2_lol %>%
hca_prev() %>%
lol_pull("hits[*].projects[*].projectTitle")
## [1] "1.3 Million Brain Cells from E18 Mice"
## [2] "A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra"
## [3] "A Cellular Atlas of Pitx2-Dependent Cardiac Development."
## [4] "A Protocol for Revealing Oral Neutrophil Heterogeneity by Single-Cell Immune Profiling in Human Saliva"
## [5] "A Single-Cell Atlas of the Human Healthy Airways."Much like projects() and files(), samples() and bundles() allow you to
provide a filter object and additional criteria to retrieve data in the
form of samples and bundles respectively
heart_filters <- filters(organ = list(is = "heart"))
heart_samples <- samples(filters = heart_filters, size = 4)
heart_samples
## # A tibble: 4 × 6
## entryId projectTitle genusSpecies disease format count
## <chr> <chr> <chr> <chr> <list> <lis>
## 1 012c52ff-4770-4c0c-8c2e-c348da… A Cellular … Mus musculus normal <chr> <int>
## 2 035db5b9-a219-4df8-bfc9-117cd0… A Cellular … Mus musculus normal <chr> <int>
## 3 09e425f7-22d7-487e-b78b-78b449… A Cellular … Mus musculus normal <chr> <int>
## 4 2273e44d-9fbc-4c13-8cb3-3caf8a… A Cellular … Mus musculus normal <chr> <int>
heart_bundles <- bundles(filters = heart_filters, size = 4)
heart_bundles
## # A tibble: 4 × 6
## projectTitle genusSpecies samples files bundleUuid bundleVersion
## <chr> <chr> <list> <lis> <chr> <chr>
## 1 A Cellular Atlas of Pitx2… Mus musculus <chr> <chr> 0d391bd1-… 2021-02-26T0…
## 2 A Cellular Atlas of Pitx2… Mus musculus <chr> <chr> 165a2df1-… 2021-02-26T0…
## 3 A Cellular Atlas of Pitx2… Mus musculus <chr> <chr> 166c1b1a-… 2020-08-04T1…
## 4 A Cellular Atlas of Pitx2… Mus musculus <chr> <chr> 18bad6b1-… 2021-02-26T0…HCA experiments are organized into catalogs, each of which can be summarized
with the summary() function
heart_filters <- filters(organ = list(is = "heart"))
summary(filters = heart_filters, type = "fileTypeSummaries")
## # A tibble: 11 × 3
## format count totalSize
## <chr> <int> <dbl>
## 1 fastq.gz 28284 6670325013979
## 2 loom 169 355865926256
## 3 bam 164 3284598129743
## 4 tsv.gz 49 49919933
## 5 mtx.gz 24 479611217
## 6 bed.gz 6 3332206567
## 7 .txt 4 80206910
## 8 RDS 3 301293176
## 9 Rds 3 2637887113
## 10 h5ad 2 2027243221
## 11 h5ad.zip 1 15510167649
first_catalog <- catalogs()[1]
summary(type = "overview", catalog = first_catalog)
## # A tibble: 9 × 2
## name value
## <chr> <dbl>
## 1 projectCount 2.08e 2
## 2 specimenCount 1.03e 4
## 3 speciesCount 3 e 0
## 4 fileCount 4.59e 5
## 5 totalFileSize 1.34e14
## 6 donorCount 2.70e 3
## 7 labCount 3.4 e 2
## 8 totalCellCount 2.09e 7
## 9 projectEstimatedCellCount 2.19e 7Each project, file, sample, and bundles has its own unique ID by which, in conjunction with its catalog, can be to uniquely identify them.
heart_filters <- filters(organ = list(is = "heart"))
heart_projects <- projects(filters = heart_filters, size = 4)
heart_projects
## # A tibble: 4 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <chr> <list> <list>
## 1 7027adc6-c9c9-46f3-84… A Cellular … Mus musculus <chr [1]> <chr [1]>
## 2 a9301beb-e9fa-42fe-b7… A human cel… Homo sapiens <chr [14]> <chr [14]>
## 3 c31fa434-c9ed-4263-a9… A single-ce… Homo sapiens <chr [18]> <chr [18]>
## 4 ad98d3cd-26fb-4ee3-99… Cells of th… Homo sapiens <chr [1]> <chr [1]>
projectId <-
heart_projects %>%
filter(
startsWith(
projectTitle,
"Cells of the adult human"
)
) %>%
dplyr::pull(projectId)
projects_detail(uuid = projectId)
## $protocols
## $protocols[[1]]
## $protocols[[1]]$workflow
## $protocols[[1]]$workflow[[1]]
## [1] "optimus_post_processing_v1.0.0"
##
## $protocols[[1]]$workflow[[2]]
## [1] "optimus_v4.2.2"
##
##
##
## $protocols[[2]]
## $protocols[[2]]$libraryConstructionApproach
## $protocols[[2]]$libraryConstructionApproach[[1]]
## [1] "10X 3' v2 sequencing"
##
## $protocols[[2]]$libraryConstructionApproach[[2]]
## [1] "10x 3' v3 sequencing"
##
##
## $protocols[[2]]$nucleicAcidSource
## $protocols[[2]]$nucleicAcidSource[[1]]
## [1] "single cell"
##
## $protocols[[2]]$nucleicAcidSource[[2]]
## [1] "single nucleus"
##
##
##
## $protocols[[3]]
## $protocols[[3]]$instrumentManufacturerModel
## $protocols[[3]]$instrumentManufacturerModel[[1]]
## [1] "Illumina HiSeq 4000"
##
## $protocols[[3]]$instrumentManufacturerModel[[2]]
## [1] "Illumina NextSeq 500"
##
##
## $protocols[[3]]$pairedEnd
## $protocols[[3]]$pairedEnd[[1]]
## [1] FALSE
##
##
##
##
## $entryId
## [1] "ad98d3cd-26fb-4ee3-99c9-8a2ab085e737"
##
## $sources
## $sources[[1]]
## $sources[[1]]$sourceId
## [1] "5da1ec4d-a462-4bf0-9ee1-4b76d8199241"
##
## $sources[[1]]$sourceSpec
## [1] "tdr:datarepo-4a3b719a:snapshot/hca_prod_ad98d3cd26fb4ee399c98a2ab085e737__20220118_dcp2_20220121_dcp12:/0"
##
##
##
## $projects
## $projects[[1]]
## $projects[[1]]$projectId
## [1] "ad98d3cd-26fb-4ee3-99c9-8a2ab085e737"
##
## $projects[[1]]$projectTitle
## [1] "Cells of the adult human heart"
##
## $projects[[1]]$projectShortname
## [1] "HeartSingleCellsAndNucleiSeq"
##
## $projects[[1]]$laboratory
## $projects[[1]]$laboratory[[1]]
## [1] "Cardiovascular Division"
##
## $projects[[1]]$laboratory[[2]]
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$laboratory[[3]]
## [1] "Cellular Genetics"
##
## $projects[[1]]$laboratory[[4]]
## [1] "Department of Genetics"
##
## $projects[[1]]$laboratory[[5]]
## [1] "Department of Histology and Embryology of Zhongshan School of Medicine"
##
## $projects[[1]]$laboratory[[6]]
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
##
## $projects[[1]]$laboratory[[7]]
## [1] "Human Cell Atlas Data Coordination Platform"
##
## $projects[[1]]$laboratory[[8]]
## [1] "Institute of Computational Biology (ICB)"
##
## $projects[[1]]$laboratory[[9]]
## [1] "National Heart and Lung Institute"
##
##
## $projects[[1]]$estimatedCellCount
## NULL
##
## $projects[[1]]$projectDescription
## [1] "Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require deeper understanding of the healthy heart’s molecular processes. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using state-of-the-art analyses of large-scale single-cell and nuclei transcriptomes, we characterise six anatomical adult heart regions (left/right atria and ventricles, apex, interventricular septum). Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, revealing distinct atrial and ventricular subsets with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment we identify cardiac resident macrophages with inflammatory and protective transcriptional signatures. Further, inference of cell-cell interactions highlight different macrophage-fibroblast-cardiomyocyte networks between atria and ventricles that are distinct from skeletal muscle. We expect this reference human cardiac cell atlas to advance mechanistic studies of heart homeostasis and disease."
##
## $projects[[1]]$contributors
## $projects[[1]]$contributors[[1]]
## $projects[[1]]$contributors[[1]]$institution
## [1] "Cambridge Biorepository for Translational Medicine"
##
## $projects[[1]]$contributors[[1]]$contactName
## [1] "Krishnaa,T.,Mahbubani"
##
## $projects[[1]]$contributors[[1]]$projectRole
## [1] "biomaterial provider"
##
## $projects[[1]]$contributors[[1]]$laboratory
## NULL
##
## $projects[[1]]$contributors[[1]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[1]]$email
## [1] "ktam2@cam.ac.uk"
##
##
## $projects[[1]]$contributors[[2]]
## $projects[[1]]$contributors[[2]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[2]]$contactName
## [1] "Joseph,J.,Boyle"
##
## $projects[[1]]$contributors[[2]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[2]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[2]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[2]]$email
## [1] "joseph.boyle@imperial.ac.uk"
##
##
## $projects[[1]]$contributors[[3]]
## $projects[[1]]$contributors[[3]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[3]]$contactName
## [1] "Emily,,Nadelmann"
##
## $projects[[1]]$contributors[[3]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[3]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[3]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[3]]$email
## [1] "Emily_Nadelmann@hms.harvard.edu"
##
##
## $projects[[1]]$contributors[[4]]
## $projects[[1]]$contributors[[4]]$institution
## [1] "EMBL-EBI"
##
## $projects[[1]]$contributors[[4]]$contactName
## [1] "Marion,F,Shadbolt"
##
## $projects[[1]]$contributors[[4]]$projectRole
## [1] "data curator"
##
## $projects[[1]]$contributors[[4]]$laboratory
## [1] "Human Cell Atlas Data Coordination Platform"
##
## $projects[[1]]$contributors[[4]]$correspondingContributor
## [1] FALSE
##
## $projects[[1]]$contributors[[4]]$email
## [1] "mshadbolt@ebi.ac.uk"
##
##
## $projects[[1]]$contributors[[5]]
## $projects[[1]]$contributors[[5]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[5]]$contactName
## [1] "Sara,,Samari"
##
## $projects[[1]]$contributors[[5]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[5]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[5]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[5]]$email
## [1] "sara.samari13@imperial.ac.uk"
##
##
## $projects[[1]]$contributors[[6]]
## $projects[[1]]$contributors[[6]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[6]]$contactName
## [1] "Kenny,,Roberts"
##
## $projects[[1]]$contributors[[6]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[6]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[6]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[6]]$email
## [1] "kr19@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[7]]
## $projects[[1]]$contributors[[7]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[7]]$contactName
## [1] "Carlos,,Talavera-López"
##
## $projects[[1]]$contributors[[7]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[7]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[7]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[7]]$email
## [1] "ct5@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[8]]
## $projects[[1]]$contributors[[8]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[8]]$contactName
## [1] "Daniel,,DeLaughter"
##
## $projects[[1]]$contributors[[8]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[8]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[8]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[8]]$email
## [1] "Daniel_DeLaughter@hms.harvard.edu"
##
##
## $projects[[1]]$contributors[[9]]
## $projects[[1]]$contributors[[9]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[9]]$contactName
## [1] "Eric,L.,Lindberg"
##
## $projects[[1]]$contributors[[9]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[9]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[9]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[9]]$email
## [1] "Eric.Lindberg@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[10]]
## $projects[[1]]$contributors[[10]]$institution
## [1] "University of Alberta"
##
## $projects[[1]]$contributors[[10]]$contactName
## [1] "Anissa,,Viveiros"
##
## $projects[[1]]$contributors[[10]]$projectRole
## [1] "biomaterial provider"
##
## $projects[[1]]$contributors[[10]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
##
## $projects[[1]]$contributors[[10]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[10]]$email
## [1] "aviveiro@ualberta.ca"
##
##
## $projects[[1]]$contributors[[11]]
## $projects[[1]]$contributors[[11]]$institution
## [1] "HMGU"
##
## $projects[[1]]$contributors[[11]]$contactName
## [1] "Matthias,,Heinig"
##
## $projects[[1]]$contributors[[11]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[11]]$laboratory
## [1] "Institute of Computational Biology (ICB)"
##
## $projects[[1]]$contributors[[11]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[11]]$email
## [1] "matthias.heinig@helmholtz-muenchen.de"
##
##
## $projects[[1]]$contributors[[12]]
## $projects[[1]]$contributors[[12]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[12]]$contactName
## [1] "Liz,,Tuck"
##
## $projects[[1]]$contributors[[12]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[12]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[12]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[12]]$email
## [1] "et2@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[13]]
## $projects[[1]]$contributors[[13]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[13]]$contactName
## [1] "Giannino,,Patone"
##
## $projects[[1]]$contributors[[13]]$projectRole
## [1] "computational scientist"
##
## $projects[[1]]$contributors[[13]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[13]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[13]]$email
## [1] "Giannino.Patone@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[14]]
## $projects[[1]]$contributors[[14]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[14]]$contactName
## [1] "Michael,,Lee"
##
## $projects[[1]]$contributors[[14]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[14]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[14]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[14]]$email
## [1] "michael.lee@imperial.ac.uk"
##
##
## $projects[[1]]$contributors[[15]]
## $projects[[1]]$contributors[[15]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[15]]$contactName
## [1] "Omer,,Bayraktar"
##
## $projects[[1]]$contributors[[15]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[15]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[15]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[15]]$email
## [1] "ob5@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[16]]
## $projects[[1]]$contributors[[16]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[16]]$contactName
## [1] "Monika,,Litviňuková"
##
## $projects[[1]]$contributors[[16]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[16]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[16]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[16]]$email
## [1] "monika.litvinukova@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[17]]
## $projects[[1]]$contributors[[17]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[17]]$contactName
## [1] "Catherine,L.,Worth"
##
## $projects[[1]]$contributors[[17]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[17]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[17]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[17]]$email
## [1] "catherine.sargent@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[18]]
## $projects[[1]]$contributors[[18]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[18]]$contactName
## [1] "Krzysztof,,Polanski"
##
## $projects[[1]]$contributors[[18]]$projectRole
## [1] "computational scientist"
##
## $projects[[1]]$contributors[[18]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[18]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[18]]$email
## [1] "kp9@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[19]]
## $projects[[1]]$contributors[[19]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[19]]$contactName
## [1] "Hiroko,,Wakimoto"
##
## $projects[[1]]$contributors[[19]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[19]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[19]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[19]]$email
## [1] "hwakimoto@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[20]]
## $projects[[1]]$contributors[[20]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[20]]$contactName
## [1] "Michela,,Noseda"
##
## $projects[[1]]$contributors[[20]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[20]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[20]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[20]]$email
## [1] "m.noseda@imperial.ac.uk"
##
##
## $projects[[1]]$contributors[[21]]
## $projects[[1]]$contributors[[21]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[21]]$contactName
## [1] "Masatoshi,,Kanda"
##
## $projects[[1]]$contributors[[21]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[21]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[21]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[21]]$email
## [1] "masatoshi.kanda@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[22]]
## $projects[[1]]$contributors[[22]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[22]]$contactName
## [1] "Sarah,A.,Teichmann"
##
## $projects[[1]]$contributors[[22]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[22]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[22]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[22]]$email
## [1] "st9@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[23]]
## $projects[[1]]$contributors[[23]]$institution
## [1] "Sun-Yat Sen University"
##
## $projects[[1]]$contributors[[23]]$contactName
## [1] "Hongbo,,Zhang"
##
## $projects[[1]]$contributors[[23]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[23]]$laboratory
## [1] "Department of Histology and Embryology of Zhongshan School of Medicine"
##
## $projects[[1]]$contributors[[23]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[23]]$email
## [1] "hz3@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[24]]
## $projects[[1]]$contributors[[24]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[24]]$contactName
## [1] "Norbert,,Hübner"
##
## $projects[[1]]$contributors[[24]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[24]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[24]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[24]]$email
## [1] "nhuebner@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[25]]
## $projects[[1]]$contributors[[25]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[25]]$contactName
## [1] "Daniel,,Reichart"
##
## $projects[[1]]$contributors[[25]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[25]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[25]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[25]]$email
## [1] "Daniel_Reichart@hms.harvard.edu"
##
##
## $projects[[1]]$contributors[[26]]
## $projects[[1]]$contributors[[26]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[26]]$contactName
## [1] "Henrike,,Maatz"
##
## $projects[[1]]$contributors[[26]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[26]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[26]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[26]]$email
## [1] "h.maatz@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[27]]
## $projects[[1]]$contributors[[27]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[27]]$contactName
## [1] "Eirini,S.,Fasouli"
##
## $projects[[1]]$contributors[[27]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[27]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[27]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[27]]$email
## [1] "ef5@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[28]]
## $projects[[1]]$contributors[[28]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[28]]$contactName
## [1] "J.,G.,Seidman"
##
## $projects[[1]]$contributors[[28]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[28]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[28]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[28]]$email
## [1] "seidman@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[29]]
## $projects[[1]]$contributors[[29]]$institution
## [1] "University of Alberta"
##
## $projects[[1]]$contributors[[29]]$contactName
## [1] "Hao,,Zhang"
##
## $projects[[1]]$contributors[[29]]$projectRole
## [1] "biomaterial provider"
##
## $projects[[1]]$contributors[[29]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
##
## $projects[[1]]$contributors[[29]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[29]]$email
## [1] "hzhang10@ualberta.ca"
##
##
## $projects[[1]]$contributors[[30]]
## $projects[[1]]$contributors[[30]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[30]]$contactName
## [1] "Joshua,M,Gorham"
##
## $projects[[1]]$contributors[[30]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[30]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[30]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[30]]$email
## [1] "jgorham@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[31]]
## $projects[[1]]$contributors[[31]]$institution
## [1] "University of Alberta"
##
## $projects[[1]]$contributors[[31]]$contactName
## [1] "Gavin,,Oudit"
##
## $projects[[1]]$contributors[[31]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[31]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
##
## $projects[[1]]$contributors[[31]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[31]]$email
## [1] "gavin.oudit@ualberta.ca"
##
##
## $projects[[1]]$contributors[[32]]
## $projects[[1]]$contributors[[32]]$institution
## [1] "Cambridge Biorepository for Translational Medicine"
##
## $projects[[1]]$contributors[[32]]$contactName
## [1] "Kourosh,,Saeb-Parsy"
##
## $projects[[1]]$contributors[[32]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[32]]$laboratory
## NULL
##
## $projects[[1]]$contributors[[32]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[32]]$email
## [1] "ks10014@cam.ac.uk"
##
##
## $projects[[1]]$contributors[[33]]
## $projects[[1]]$contributors[[33]]$institution
## [1] "Brigham and Women’s Hospital"
##
## $projects[[1]]$contributors[[33]]$contactName
## [1] "Barbara,,McDonough"
##
## $projects[[1]]$contributors[[33]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[33]]$laboratory
## [1] "Cardiovascular Division"
##
## $projects[[1]]$contributors[[33]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[33]]$email
## [1] "mcdonough@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[34]]
## $projects[[1]]$contributors[[34]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[34]]$contactName
## [1] "Christine,,Seidman"
##
## $projects[[1]]$contributors[[34]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[34]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[34]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[34]]$email
## [1] "cseidman@genetics.med.harvard.edu"
##
##
##
## $projects[[1]]$publications
## $projects[[1]]$publications[[1]]
## $projects[[1]]$publications[[1]]$publicationTitle
## [1] "Cells of the adult human heart"
##
## $projects[[1]]$publications[[1]]$officialHcaPublication
## NULL
##
## $projects[[1]]$publications[[1]]$publicationUrl
## [1] "https://www.nature.com/articles/s41586-020-2797-4"
##
## $projects[[1]]$publications[[1]]$doi
## [1] "10.1038/s41586-020-2797-4"
##
##
##
## $projects[[1]]$supplementaryLinks
## $projects[[1]]$supplementaryLinks[[1]]
## [1] "https://www.heartcellatlas.org/"
##
##
## $projects[[1]]$matrices
## $projects[[1]]$matrices$genusSpecies
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription[[1]]
## [1] "Count Matrix"
##
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$format
## [1] "loom"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$isIntermediate
## [1] FALSE
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$name
## [1] "human-heart-10XV3.loom"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$sha256
## [1] "ee31af654eb2008c8748875b117ee7eecd70ad63ed93811144fb44651144c3ca"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$size
## [1] 3255905369
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$fileSource
## [1] "DCP/2 Analysis"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$uuid
## [1] "b0cd671e-a918-51db-ba29-e127caf325c5"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$version
## [1] "2021-02-13T01:32:57.000000Z"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$matrixCellCount
## NULL
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b0cd671e-a918-51db-ba29-e127caf325c5?catalog=dcp13&version=2021-02-13T01%3A32%3A57.000000Z"
##
##
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription[[1]]
## [1] "Count Matrix"
##
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$format
## [1] "loom"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$isIntermediate
## [1] FALSE
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$name
## [1] "human-heart-10XV2.loom"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$sha256
## [1] "d38c4fe7ef2bfb28f42854e447ba65929bbcd89023211c1bff0e34674bede78e"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$size
## [1] 4398007571
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$fileSource
## [1] "DCP/2 Analysis"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "dc58c876-3de2-5264-b108-531d4e6c914a"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-15T14:15:05.000000Z"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrixCellCount
## NULL
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/dc58c876-3de2-5264-b108-531d4e6c914a?catalog=dcp13&version=2021-02-15T14%3A15%3A05.000000Z"
##
##
##
##
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription[[1]]
## [1] "Count Matrix"
##
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$format
## [1] "loom"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$isIntermediate
## [1] FALSE
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$name
## [1] "human-heart-10XV2.loom"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$sha256
## [1] "d38c4fe7ef2bfb28f42854e447ba65929bbcd89023211c1bff0e34674bede78e"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$size
## [1] 4398007571
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$fileSource
## [1] "DCP/2 Analysis"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "dc58c876-3de2-5264-b108-531d4e6c914a"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-15T14:15:05.000000Z"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrixCellCount
## NULL
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/dc58c876-3de2-5264-b108-531d4e6c914a?catalog=dcp13&version=2021-02-15T14%3A15%3A05.000000Z"
##
##
##
##
##
##
##
##
##
##
##
## $projects[[1]]$contributedAnalyses
## $projects[[1]]$contributedAnalyses$genusSpecies
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription[[1]]
## [1] "Matrix"
##
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$format
## [1] "h5ad"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$isIntermediate
## [1] FALSE
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$name
## [1] "hca_heart_global_ctl200723_freeze.h5ad"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$sha256
## [1] "80917c4e67e581ee2696691ddd4b031bf45cbc7ba77757c8a203cd88c15f9c3f"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$size
## [1] 5068859764
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$fileSource
## [1] "Contributor"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "b30d1a16-fb04-5ac7-999f-6ce9d1de0c76"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-10T17:01:03.177554Z"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrixCellCount
## NULL
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b30d1a16-fb04-5ac7-999f-6ce9d1de0c76?catalog=dcp13&version=2021-02-10T17%3A01%3A03.177554Z"
##
##
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription[[1]]
## [1] "Matrix"
##
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$format
## [1] "h5ad"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$isIntermediate
## [1] FALSE
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$name
## [1] "hca_heart_global_ctl200723_freeze.h5ad"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$sha256
## [1] "80917c4e67e581ee2696691ddd4b031bf45cbc7ba77757c8a203cd88c15f9c3f"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$size
## [1] 5068859764
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$fileSource
## [1] "Contributor"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$uuid
## [1] "b30d1a16-fb04-5ac7-999f-6ce9d1de0c76"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$version
## [1] "2021-02-10T17:01:03.177554Z"
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$matrixCellCount
## NULL
##
## $projects[[1]]$contributedAnalyses$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b30d1a16-fb04-5ac7-999f-6ce9d1de0c76?catalog=dcp13&version=2021-02-10T17%3A01%3A03.177554Z"
##
##
##
##
##
##
##
##
##
##
##
## $projects[[1]]$accessions
## $projects[[1]]$accessions[[1]]
## $projects[[1]]$accessions[[1]]$namespace
## [1] "biostudies"
##
## $projects[[1]]$accessions[[1]]$accession
## [1] "S-SUBS13"
##
##
## $projects[[1]]$accessions[[2]]
## $projects[[1]]$accessions[[2]]$namespace
## [1] "insdc_project"
##
## $projects[[1]]$accessions[[2]]$accession
## [1] "ERP123138"
##
##
## $projects[[1]]$accessions[[3]]
## $projects[[1]]$accessions[[3]]$namespace
## [1] "insdc_study"
##
## $projects[[1]]$accessions[[3]]$accession
## [1] "PRJEB39602"
##
##
##
## $projects[[1]]$accessible
## [1] TRUE
##
##
##
## $samples
## $samples[[1]]
## $samples[[1]]$sampleEntityType
## $samples[[1]]$sampleEntityType[[1]]
## [1] "specimens"
##
##
## $samples[[1]]$effectiveOrgan
## $samples[[1]]$effectiveOrgan[[1]]
## [1] "heart"
##
##
## $samples[[1]]$id
## $samples[[1]]$id[[1]]
## [1] "CBTM-361B_AX"
##
## $samples[[1]]$id[[2]]
## [1] "CBTM-361B_LA"
##
## $samples[[1]]$id[[3]]
## [1] "CBTM-361B_LV"
##
## $samples[[1]]$id[[4]]
## [1] "CBTM-361B_RV"
##
## $samples[[1]]$id[[5]]
## [1] "CBTM-362C_AX"
##
## $samples[[1]]$id[[6]]
## [1] "CBTM-362C_LA"
##
## $samples[[1]]$id[[7]]
## [1] "CBTM-362C_LV"
##
## $samples[[1]]$id[[8]]
## [1] "CBTM-362C_RA"
##
## $samples[[1]]$id[[9]]
## [1] "CBTM-362C_RV"
##
## $samples[[1]]$id[[10]]
## [1] "CBTM-362C_SP"
##
## $samples[[1]]$id[[11]]
## [1] "CBTM-364B_AX"
##
## $samples[[1]]$id[[12]]
## [1] "CBTM-364B_LA"
##
## $samples[[1]]$id[[13]]
## [1] "CBTM-364B_LV"
##
## $samples[[1]]$id[[14]]
## [1] "CBTM-364B_RA"
##
## $samples[[1]]$id[[15]]
## [1] "CBTM-364B_RV"
##
## $samples[[1]]$id[[16]]
## [1] "CBTM-364B_SP"
##
## $samples[[1]]$id[[17]]
## [1] "CBTM-386C_AX"
##
## $samples[[1]]$id[[18]]
## [1] "CBTM-386C_LA"
##
## $samples[[1]]$id[[19]]
## [1] "CBTM-386C_LV"
##
## $samples[[1]]$id[[20]]
## [1] "CBTM-386C_RA"
##
## $samples[[1]]$id[[21]]
## [1] "CBTM-386C_RV"
##
## $samples[[1]]$id[[22]]
## [1] "CBTM-386C_SP"
##
## $samples[[1]]$id[[23]]
## [1] "CBTM-390C_AX"
##
## $samples[[1]]$id[[24]]
## [1] "CBTM-390C_LA"
##
## $samples[[1]]$id[[25]]
## [1] "CBTM-390C_LV"
##
## $samples[[1]]$id[[26]]
## [1] "CBTM-390C_RA"
##
## $samples[[1]]$id[[27]]
## [1] "CBTM-390C_RV"
##
## $samples[[1]]$id[[28]]
## [1] "CBTM-390C_SP"
##
## $samples[[1]]$id[[29]]
## [1] "CBTM-417C_AX"
##
## $samples[[1]]$id[[30]]
## [1] "CBTM-417C_LA"
##
## $samples[[1]]$id[[31]]
## [1] "CBTM-417C_LV"
##
## $samples[[1]]$id[[32]]
## [1] "CBTM-417C_RA"
##
## $samples[[1]]$id[[33]]
## [1] "CBTM-417C_RV"
##
## $samples[[1]]$id[[34]]
## [1] "CBTM-417C_SP"
##
## $samples[[1]]$id[[35]]
## [1] "CBTM-423C_AX"
##
## $samples[[1]]$id[[36]]
## [1] "CBTM-423C_LA"
##
## $samples[[1]]$id[[37]]
## [1] "CBTM-423C_LV"
##
## $samples[[1]]$id[[38]]
## [1] "CBTM-423C_RA"
##
## $samples[[1]]$id[[39]]
## [1] "CBTM-423C_RV"
##
## $samples[[1]]$id[[40]]
## [1] "CBTM-423C_SP"
##
## $samples[[1]]$id[[41]]
## [1] "CBTM-473C_AX"
##
## $samples[[1]]$id[[42]]
## [1] "CBTM-473C_LA"
##
## $samples[[1]]$id[[43]]
## [1] "CBTM-473C_LV"
##
## $samples[[1]]$id[[44]]
## [1] "CBTM-473C_RA"
##
## $samples[[1]]$id[[45]]
## [1] "CBTM-473C_RV"
##
## $samples[[1]]$id[[46]]
## [1] "CBTM-473C_SP"
##
## $samples[[1]]$id[[47]]
## [1] "H0015_AX"
##
## $samples[[1]]$id[[48]]
## [1] "H0015_LA"
##
## $samples[[1]]$id[[49]]
## [1] "H0015_LV"
##
## $samples[[1]]$id[[50]]
## [1] "H0015_RA"
##
## $samples[[1]]$id[[51]]
## [1] "H0015_RV"
##
## $samples[[1]]$id[[52]]
## [1] "H0015_SP"
##
## $samples[[1]]$id[[53]]
## [1] "H0020_AX"
##
## $samples[[1]]$id[[54]]
## [1] "H0020_LA"
##
## $samples[[1]]$id[[55]]
## [1] "H0020_LV"
##
## $samples[[1]]$id[[56]]
## [1] "H0020_RA"
##
## $samples[[1]]$id[[57]]
## [1] "H0020_RV"
##
## $samples[[1]]$id[[58]]
## [1] "H0020_SP"
##
## $samples[[1]]$id[[59]]
## [1] "H0025_AX"
##
## $samples[[1]]$id[[60]]
## [1] "H0025_LA"
##
## $samples[[1]]$id[[61]]
## [1] "H0025_LV"
##
## $samples[[1]]$id[[62]]
## [1] "H0025_RA"
##
## $samples[[1]]$id[[63]]
## [1] "H0025_RV"
##
## $samples[[1]]$id[[64]]
## [1] "H0025_SP"
##
## $samples[[1]]$id[[65]]
## [1] "H0026_AX"
##
## $samples[[1]]$id[[66]]
## [1] "H0026_LA"
##
## $samples[[1]]$id[[67]]
## [1] "H0026_LV"
##
## $samples[[1]]$id[[68]]
## [1] "H0026_RA"
##
## $samples[[1]]$id[[69]]
## [1] "H0026_RV"
##
## $samples[[1]]$id[[70]]
## [1] "H0026_SP"
##
## $samples[[1]]$id[[71]]
## [1] "H0035_AX"
##
## $samples[[1]]$id[[72]]
## [1] "H0035_LA"
##
## $samples[[1]]$id[[73]]
## [1] "H0035_LV"
##
## $samples[[1]]$id[[74]]
## [1] "H0035_RA"
##
## $samples[[1]]$id[[75]]
## [1] "H0035_RV"
##
## $samples[[1]]$id[[76]]
## [1] "H0035_SP"
##
## $samples[[1]]$id[[77]]
## [1] "H0037_AX"
##
## $samples[[1]]$id[[78]]
## [1] "H0037_LA"
##
## $samples[[1]]$id[[79]]
## [1] "H0037_LV"
##
## $samples[[1]]$id[[80]]
## [1] "H0037_RA"
##
## $samples[[1]]$id[[81]]
## [1] "H0037_RV"
##
## $samples[[1]]$id[[82]]
## [1] "H0037_SP"
##
##
## $samples[[1]]$organ
## $samples[[1]]$organ[[1]]
## [1] "heart"
##
##
## $samples[[1]]$organPart
## $samples[[1]]$organPart[[1]]
## [1] "apex of heart"
##
## $samples[[1]]$organPart[[2]]
## [1] "heart left ventricle"
##
## $samples[[1]]$organPart[[3]]
## [1] "heart right ventricle"
##
## $samples[[1]]$organPart[[4]]
## [1] "interventricular septum"
##
## $samples[[1]]$organPart[[5]]
## [1] "left cardiac atrium"
##
## $samples[[1]]$organPart[[6]]
## [1] "right cardiac atrium"
##
##
## $samples[[1]]$disease
## $samples[[1]]$disease[[1]]
## NULL
##
##
## $samples[[1]]$preservationMethod
## $samples[[1]]$preservationMethod[[1]]
## NULL
##
##
## $samples[[1]]$source
## $samples[[1]]$source[[1]]
## [1] "specimen_from_organism"
##
##
##
##
## $specimens
## $specimens[[1]]
## $specimens[[1]]$id
## $specimens[[1]]$id[[1]]
## [1] "CBTM-361B_AX"
##
## $specimens[[1]]$id[[2]]
## [1] "CBTM-361B_LA"
##
## $specimens[[1]]$id[[3]]
## [1] "CBTM-361B_LV"
##
## $specimens[[1]]$id[[4]]
## [1] "CBTM-361B_RV"
##
## $specimens[[1]]$id[[5]]
## [1] "CBTM-362C_AX"
##
## $specimens[[1]]$id[[6]]
## [1] "CBTM-362C_LA"
##
## $specimens[[1]]$id[[7]]
## [1] "CBTM-362C_LV"
##
## $specimens[[1]]$id[[8]]
## [1] "CBTM-362C_RA"
##
## $specimens[[1]]$id[[9]]
## [1] "CBTM-362C_RV"
##
## $specimens[[1]]$id[[10]]
## [1] "CBTM-362C_SP"
##
## $specimens[[1]]$id[[11]]
## [1] "CBTM-364B_AX"
##
## $specimens[[1]]$id[[12]]
## [1] "CBTM-364B_LA"
##
## $specimens[[1]]$id[[13]]
## [1] "CBTM-364B_LV"
##
## $specimens[[1]]$id[[14]]
## [1] "CBTM-364B_RA"
##
## $specimens[[1]]$id[[15]]
## [1] "CBTM-364B_RV"
##
## $specimens[[1]]$id[[16]]
## [1] "CBTM-364B_SP"
##
## $specimens[[1]]$id[[17]]
## [1] "CBTM-386C_AX"
##
## $specimens[[1]]$id[[18]]
## [1] "CBTM-386C_LA"
##
## $specimens[[1]]$id[[19]]
## [1] "CBTM-386C_LV"
##
## $specimens[[1]]$id[[20]]
## [1] "CBTM-386C_RA"
##
## $specimens[[1]]$id[[21]]
## [1] "CBTM-386C_RV"
##
## $specimens[[1]]$id[[22]]
## [1] "CBTM-386C_SP"
##
## $specimens[[1]]$id[[23]]
## [1] "CBTM-390C_AX"
##
## $specimens[[1]]$id[[24]]
## [1] "CBTM-390C_LA"
##
## $specimens[[1]]$id[[25]]
## [1] "CBTM-390C_LV"
##
## $specimens[[1]]$id[[26]]
## [1] "CBTM-390C_RA"
##
## $specimens[[1]]$id[[27]]
## [1] "CBTM-390C_RV"
##
## $specimens[[1]]$id[[28]]
## [1] "CBTM-390C_SP"
##
## $specimens[[1]]$id[[29]]
## [1] "CBTM-417C_AX"
##
## $specimens[[1]]$id[[30]]
## [1] "CBTM-417C_LA"
##
## $specimens[[1]]$id[[31]]
## [1] "CBTM-417C_LV"
##
## $specimens[[1]]$id[[32]]
## [1] "CBTM-417C_RA"
##
## $specimens[[1]]$id[[33]]
## [1] "CBTM-417C_RV"
##
## $specimens[[1]]$id[[34]]
## [1] "CBTM-417C_SP"
##
## $specimens[[1]]$id[[35]]
## [1] "CBTM-423C_AX"
##
## $specimens[[1]]$id[[36]]
## [1] "CBTM-423C_LA"
##
## $specimens[[1]]$id[[37]]
## [1] "CBTM-423C_LV"
##
## $specimens[[1]]$id[[38]]
## [1] "CBTM-423C_RA"
##
## $specimens[[1]]$id[[39]]
## [1] "CBTM-423C_RV"
##
## $specimens[[1]]$id[[40]]
## [1] "CBTM-423C_SP"
##
## $specimens[[1]]$id[[41]]
## [1] "CBTM-473C_AX"
##
## $specimens[[1]]$id[[42]]
## [1] "CBTM-473C_LA"
##
## $specimens[[1]]$id[[43]]
## [1] "CBTM-473C_LV"
##
## $specimens[[1]]$id[[44]]
## [1] "CBTM-473C_RA"
##
## $specimens[[1]]$id[[45]]
## [1] "CBTM-473C_RV"
##
## $specimens[[1]]$id[[46]]
## [1] "CBTM-473C_SP"
##
## $specimens[[1]]$id[[47]]
## [1] "H0015_AX"
##
## $specimens[[1]]$id[[48]]
## [1] "H0015_LA"
##
## $specimens[[1]]$id[[49]]
## [1] "H0015_LV"
##
## $specimens[[1]]$id[[50]]
## [1] "H0015_RA"
##
## $specimens[[1]]$id[[51]]
## [1] "H0015_RV"
##
## $specimens[[1]]$id[[52]]
## [1] "H0015_SP"
##
## $specimens[[1]]$id[[53]]
## [1] "H0020_AX"
##
## $specimens[[1]]$id[[54]]
## [1] "H0020_LA"
##
## $specimens[[1]]$id[[55]]
## [1] "H0020_LV"
##
## $specimens[[1]]$id[[56]]
## [1] "H0020_RA"
##
## $specimens[[1]]$id[[57]]
## [1] "H0020_RV"
##
## $specimens[[1]]$id[[58]]
## [1] "H0020_SP"
##
## $specimens[[1]]$id[[59]]
## [1] "H0025_AX"
##
## $specimens[[1]]$id[[60]]
## [1] "H0025_LA"
##
## $specimens[[1]]$id[[61]]
## [1] "H0025_LV"
##
## $specimens[[1]]$id[[62]]
## [1] "H0025_RA"
##
## $specimens[[1]]$id[[63]]
## [1] "H0025_RV"
##
## $specimens[[1]]$id[[64]]
## [1] "H0025_SP"
##
## $specimens[[1]]$id[[65]]
## [1] "H0026_AX"
##
## $specimens[[1]]$id[[66]]
## [1] "H0026_LA"
##
## $specimens[[1]]$id[[67]]
## [1] "H0026_LV"
##
## $specimens[[1]]$id[[68]]
## [1] "H0026_RA"
##
## $specimens[[1]]$id[[69]]
## [1] "H0026_RV"
##
## $specimens[[1]]$id[[70]]
## [1] "H0026_SP"
##
## $specimens[[1]]$id[[71]]
## [1] "H0035_AX"
##
## $specimens[[1]]$id[[72]]
## [1] "H0035_LA"
##
## $specimens[[1]]$id[[73]]
## [1] "H0035_LV"
##
## $specimens[[1]]$id[[74]]
## [1] "H0035_RA"
##
## $specimens[[1]]$id[[75]]
## [1] "H0035_RV"
##
## $specimens[[1]]$id[[76]]
## [1] "H0035_SP"
##
## $specimens[[1]]$id[[77]]
## [1] "H0037_AX"
##
## $specimens[[1]]$id[[78]]
## [1] "H0037_LA"
##
## $specimens[[1]]$id[[79]]
## [1] "H0037_LV"
##
## $specimens[[1]]$id[[80]]
## [1] "H0037_RA"
##
## $specimens[[1]]$id[[81]]
## [1] "H0037_RV"
##
## $specimens[[1]]$id[[82]]
## [1] "H0037_SP"
##
##
## $specimens[[1]]$organ
## $specimens[[1]]$organ[[1]]
## [1] "heart"
##
##
## $specimens[[1]]$organPart
## $specimens[[1]]$organPart[[1]]
## [1] "apex of heart"
##
## $specimens[[1]]$organPart[[2]]
## [1] "heart left ventricle"
##
## $specimens[[1]]$organPart[[3]]
## [1] "heart right ventricle"
##
## $specimens[[1]]$organPart[[4]]
## [1] "interventricular septum"
##
## $specimens[[1]]$organPart[[5]]
## [1] "left cardiac atrium"
##
## $specimens[[1]]$organPart[[6]]
## [1] "right cardiac atrium"
##
##
## $specimens[[1]]$disease
## $specimens[[1]]$disease[[1]]
## NULL
##
##
## $specimens[[1]]$preservationMethod
## $specimens[[1]]$preservationMethod[[1]]
## NULL
##
##
## $specimens[[1]]$source
## $specimens[[1]]$source[[1]]
## [1] "specimen_from_organism"
##
##
##
##
## $cellLines
## list()
##
## $donorOrganisms
## $donorOrganisms[[1]]
## $donorOrganisms[[1]]$id
## $donorOrganisms[[1]]$id[[1]]
## [1] "CBTM-361B"
##
## $donorOrganisms[[1]]$id[[2]]
## [1] "CBTM-362C"
##
## $donorOrganisms[[1]]$id[[3]]
## [1] "CBTM-364B"
##
## $donorOrganisms[[1]]$id[[4]]
## [1] "CBTM-386C"
##
## $donorOrganisms[[1]]$id[[5]]
## [1] "CBTM-390C"
##
## $donorOrganisms[[1]]$id[[6]]
## [1] "CBTM-417C"
##
## $donorOrganisms[[1]]$id[[7]]
## [1] "CBTM-423C"
##
## $donorOrganisms[[1]]$id[[8]]
## [1] "CBTM-473C"
##
## $donorOrganisms[[1]]$id[[9]]
## [1] "H0015"
##
## $donorOrganisms[[1]]$id[[10]]
## [1] "H0020"
##
## $donorOrganisms[[1]]$id[[11]]
## [1] "H0025"
##
## $donorOrganisms[[1]]$id[[12]]
## [1] "H0026"
##
## $donorOrganisms[[1]]$id[[13]]
## [1] "H0035"
##
## $donorOrganisms[[1]]$id[[14]]
## [1] "H0037"
##
##
## $donorOrganisms[[1]]$donorCount
## [1] 14
##
## $donorOrganisms[[1]]$developmentStage
## $donorOrganisms[[1]]$developmentStage[[1]]
## [1] "adult"
##
## $donorOrganisms[[1]]$developmentStage[[2]]
## [1] "human adult stage"
##
##
## $donorOrganisms[[1]]$genusSpecies
## $donorOrganisms[[1]]$genusSpecies[[1]]
## [1] "Homo sapiens"
##
##
## $donorOrganisms[[1]]$organismAge
## $donorOrganisms[[1]]$organismAge[[1]]
## $donorOrganisms[[1]]$organismAge[[1]]$value
## [1] "40-45"
##
## $donorOrganisms[[1]]$organismAge[[1]]$unit
## [1] "year"
##
##
## $donorOrganisms[[1]]$organismAge[[2]]
## $donorOrganisms[[1]]$organismAge[[2]]$value
## [1] "45-50"
##
## $donorOrganisms[[1]]$organismAge[[2]]$unit
## [1] "year"
##
##
## $donorOrganisms[[1]]$organismAge[[3]]
## $donorOrganisms[[1]]$organismAge[[3]]$value
## [1] "50-55"
##
## $donorOrganisms[[1]]$organismAge[[3]]$unit
## [1] "year"
##
##
## $donorOrganisms[[1]]$organismAge[[4]]
## $donorOrganisms[[1]]$organismAge[[4]]$value
## [1] "55-60"
##
## $donorOrganisms[[1]]$organismAge[[4]]$unit
## [1] "year"
##
##
## $donorOrganisms[[1]]$organismAge[[5]]
## $donorOrganisms[[1]]$organismAge[[5]]$value
## [1] "60-65"
##
## $donorOrganisms[[1]]$organismAge[[5]]$unit
## [1] "year"
##
##
## $donorOrganisms[[1]]$organismAge[[6]]
## $donorOrganisms[[1]]$organismAge[[6]]$value
## [1] "65-70"
##
## $donorOrganisms[[1]]$organismAge[[6]]$unit
## [1] "year"
##
##
## $donorOrganisms[[1]]$organismAge[[7]]
## $donorOrganisms[[1]]$organismAge[[7]]$value
## [1] "70-75"
##
## $donorOrganisms[[1]]$organismAge[[7]]$unit
## [1] "year"
##
##
##
## $donorOrganisms[[1]]$organismAgeRange
## $donorOrganisms[[1]]$organismAgeRange[[1]]
## $donorOrganisms[[1]]$organismAgeRange[[1]]$gte
## [1] 1261440000
##
## $donorOrganisms[[1]]$organismAgeRange[[1]]$lte
## [1] 1419120000
##
##
## $donorOrganisms[[1]]$organismAgeRange[[2]]
## $donorOrganisms[[1]]$organismAgeRange[[2]]$gte
## [1] 1419120000
##
## $donorOrganisms[[1]]$organismAgeRange[[2]]$lte
## [1] 1576800000
##
##
## $donorOrganisms[[1]]$organismAgeRange[[3]]
## $donorOrganisms[[1]]$organismAgeRange[[3]]$gte
## [1] 1576800000
##
## $donorOrganisms[[1]]$organismAgeRange[[3]]$lte
## [1] 1734480000
##
##
## $donorOrganisms[[1]]$organismAgeRange[[4]]
## $donorOrganisms[[1]]$organismAgeRange[[4]]$gte
## [1] 1734480000
##
## $donorOrganisms[[1]]$organismAgeRange[[4]]$lte
## [1] 1892160000
##
##
## $donorOrganisms[[1]]$organismAgeRange[[5]]
## $donorOrganisms[[1]]$organismAgeRange[[5]]$gte
## [1] 1892160000
##
## $donorOrganisms[[1]]$organismAgeRange[[5]]$lte
## [1] 2049840000
##
##
## $donorOrganisms[[1]]$organismAgeRange[[6]]
## $donorOrganisms[[1]]$organismAgeRange[[6]]$gte
## [1] 2049840000
##
## $donorOrganisms[[1]]$organismAgeRange[[6]]$lte
## [1] 2207520000
##
##
## $donorOrganisms[[1]]$organismAgeRange[[7]]
## $donorOrganisms[[1]]$organismAgeRange[[7]]$gte
## [1] 2207520000
##
## $donorOrganisms[[1]]$organismAgeRange[[7]]$lte
## [1] 2365200000
##
##
##
## $donorOrganisms[[1]]$biologicalSex
## $donorOrganisms[[1]]$biologicalSex[[1]]
## [1] "female"
##
## $donorOrganisms[[1]]$biologicalSex[[2]]
## [1] "male"
##
##
## $donorOrganisms[[1]]$disease
## $donorOrganisms[[1]]$disease[[1]]
## [1] "Diabetes"
##
## $donorOrganisms[[1]]$disease[[2]]
## [1] "diabetes mellitus (disease)"
##
## $donorOrganisms[[1]]$disease[[3]]
## [1] "hypertension"
##
## $donorOrganisms[[1]]$disease[[4]]
## [1] "normal"
##
##
##
##
## $organoids
## list()
##
## $cellSuspensions
## $cellSuspensions[[1]]
## $cellSuspensions[[1]]$organ
## $cellSuspensions[[1]]$organ[[1]]
## [1] "heart"
##
##
## $cellSuspensions[[1]]$organPart
## $cellSuspensions[[1]]$organPart[[1]]
## [1] "apex of heart"
##
## $cellSuspensions[[1]]$organPart[[2]]
## [1] "heart left ventricle"
##
## $cellSuspensions[[1]]$organPart[[3]]
## [1] "heart right ventricle"
##
## $cellSuspensions[[1]]$organPart[[4]]
## [1] "interventricular septum"
##
## $cellSuspensions[[1]]$organPart[[5]]
## [1] "left cardiac atrium"
##
## $cellSuspensions[[1]]$organPart[[6]]
## [1] "right cardiac atrium"
##
##
## $cellSuspensions[[1]]$selectedCellType
## $cellSuspensions[[1]]$selectedCellType[[1]]
## NULL
##
##
## $cellSuspensions[[1]]$totalCells
## [1] 791000
##
##
##
## $dates
## $dates[[1]]
## $dates[[1]]$aggregateLastModifiedDate
## [1] "2021-02-26T16:30:00.000000Z"
##
## $dates[[1]]$aggregateSubmissionDate
## [1] "2020-07-22T12:26:56.289000Z"
##
## $dates[[1]]$aggregateUpdateDate
## [1] "2021-02-26T16:30:00.000000Z"
##
## $dates[[1]]$lastModifiedDate
## [1] "2020-10-19T16:31:10.620000Z"
##
## $dates[[1]]$submissionDate
## [1] "2020-07-22T12:26:56.289000Z"
##
## $dates[[1]]$updateDate
## [1] "2020-10-19T16:31:10.620000Z"
##
##
##
## $fileTypeSummaries
## $fileTypeSummaries[[1]]
## $fileTypeSummaries[[1]]$format
## [1] "fastq.gz"
##
## $fileTypeSummaries[[1]]$fileSource
## $fileTypeSummaries[[1]]$fileSource[[1]]
## NULL
##
##
## $fileTypeSummaries[[1]]$count
## [1] 768
##
## $fileTypeSummaries[[1]]$totalSize
## [1] 3.05423e+12
##
## $fileTypeSummaries[[1]]$matrixCellCount
## NULL
##
## $fileTypeSummaries[[1]]$isIntermediate
## NULL
##
## $fileTypeSummaries[[1]]$contentDescription
## $fileTypeSummaries[[1]]$contentDescription[[1]]
## [1] "DNA sequence"
##
##
##
## $fileTypeSummaries[[2]]
## $fileTypeSummaries[[2]]$format
## [1] "loom"
##
## $fileTypeSummaries[[2]]$fileSource
## $fileTypeSummaries[[2]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
##
##
## $fileTypeSummaries[[2]]$count
## [1] 148
##
## $fileTypeSummaries[[2]]$totalSize
## [1] 286860224345
##
## $fileTypeSummaries[[2]]$matrixCellCount
## NULL
##
## $fileTypeSummaries[[2]]$isIntermediate
## [1] TRUE
##
## $fileTypeSummaries[[2]]$contentDescription
## $fileTypeSummaries[[2]]$contentDescription[[1]]
## [1] "Count Matrix"
##
##
##
## $fileTypeSummaries[[3]]
## $fileTypeSummaries[[3]]$format
## [1] "bam"
##
## $fileTypeSummaries[[3]]$fileSource
## $fileTypeSummaries[[3]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
##
##
## $fileTypeSummaries[[3]]$count
## [1] 148
##
## $fileTypeSummaries[[3]]$totalSize
## [1] 2.703466e+12
##
## $fileTypeSummaries[[3]]$matrixCellCount
## NULL
##
## $fileTypeSummaries[[3]]$isIntermediate
## NULL
##
## $fileTypeSummaries[[3]]$contentDescription
## $fileTypeSummaries[[3]]$contentDescription[[1]]
## NULL
##
##
##
## $fileTypeSummaries[[4]]
## $fileTypeSummaries[[4]]$format
## [1] "loom"
##
## $fileTypeSummaries[[4]]$fileSource
## $fileTypeSummaries[[4]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
##
##
## $fileTypeSummaries[[4]]$count
## [1] 2
##
## $fileTypeSummaries[[4]]$totalSize
## [1] 7653912940
##
## $fileTypeSummaries[[4]]$matrixCellCount
## NULL
##
## $fileTypeSummaries[[4]]$isIntermediate
## [1] FALSE
##
## $fileTypeSummaries[[4]]$contentDescription
## $fileTypeSummaries[[4]]$contentDescription[[1]]
## [1] "Count Matrix"
##
##
##
## $fileTypeSummaries[[5]]
## $fileTypeSummaries[[5]]$format
## [1] "h5ad"
##
## $fileTypeSummaries[[5]]$fileSource
## $fileTypeSummaries[[5]]$fileSource[[1]]
## [1] "Contributor"
##
##
## $fileTypeSummaries[[5]]$count
## [1] 1
##
## $fileTypeSummaries[[5]]$totalSize
## [1] 5068859764
##
## $fileTypeSummaries[[5]]$matrixCellCount
## NULL
##
## $fileTypeSummaries[[5]]$isIntermediate
## [1] FALSE
##
## $fileTypeSummaries[[5]]$contentDescription
## $fileTypeSummaries[[5]]$contentDescription[[1]]
## [1] "Matrix"See the accompanying “Human Cell Atlas Manifests” vignette on details pertaining to the use of the manifest endpoint and further annotation of .loom files
sessionInfo()
## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] httr_1.4.2 hca_1.2.3
## [3] LoomExperiment_1.12.0 BiocIO_1.4.0
## [5] rhdf5_2.38.1 SingleCellExperiment_1.16.0
## [7] SummarizedExperiment_1.24.0 Biobase_2.54.0
## [9] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
## [11] IRanges_2.28.0 S4Vectors_0.32.4
## [13] BiocGenerics_0.40.0 MatrixGenerics_1.6.0
## [15] matrixStats_0.61.0 dplyr_1.0.8
## [17] BiocStyle_2.22.0
##
## loaded via a namespace (and not attached):
## [1] tidyr_1.2.0 sass_0.4.1 vroom_1.5.7
## [4] bit64_4.0.5 jsonlite_1.8.0 bslib_0.3.1
## [7] assertthat_0.2.1 BiocManager_1.30.16 BiocFileCache_2.2.1
## [10] blob_1.2.2 GenomeInfoDbData_1.2.7 yaml_2.3.5
## [13] pillar_1.7.0 RSQLite_2.2.12 lattice_0.20-45
## [16] glue_1.6.2 digest_0.6.29 XVector_0.34.0
## [19] htmltools_0.5.2 Matrix_1.4-1 pkgconfig_2.0.3
## [22] bookdown_0.25 zlibbioc_1.40.0 purrr_0.3.4
## [25] HDF5Array_1.22.1 tzdb_0.3.0 tibble_3.1.6
## [28] generics_0.1.2 ellipsis_0.3.2 withr_2.5.0
## [31] cachem_1.0.6 cli_3.2.0 magrittr_2.0.3
## [34] crayon_1.5.1 memoise_2.0.1 evaluate_0.15
## [37] fansi_1.0.3 tools_4.1.3 hms_1.1.1
## [40] formatR_1.12 lifecycle_1.0.1 stringr_1.4.0
## [43] Rhdf5lib_1.16.0 DelayedArray_0.20.0 lambda.r_1.2.4
## [46] compiler_4.1.3 jquerylib_0.1.4 rlang_1.0.2
## [49] futile.logger_1.4.3 grid_4.1.3 RCurl_1.98-1.6
## [52] rhdf5filters_1.6.0 rappdirs_0.3.3 bitops_1.0-7
## [55] rmarkdown_2.13 DBI_1.1.2 curl_4.3.2
## [58] R6_2.5.1 knitr_1.38 fastmap_1.1.0
## [61] bit_4.0.4 utf8_1.2.2 filelock_1.0.2
## [64] futile.options_1.0.1 readr_2.1.2 stringi_1.7.6
## [67] parallel_4.1.3 Rcpp_1.0.8.3 vctrs_0.4.0
## [70] dbplyr_2.1.1 tidyselect_1.1.2 xfun_0.30