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: 124 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 74b6d569-3b1… 1.3 Million Brain C… <chr [1]> <chr [1]> <chr [1]>
## 2 53c53cd4-812… A Cellular Anatomy … <chr [1]> <chr [1]> <chr [1]>
## 3 7027adc6-c9c… A Cellular Atlas of… <chr [1]> <chr [1]> <chr [1]>
## 4 60ea42e1-af4… A Protocol for Reve… <chr [1]> <chr [1]> <chr [1]>
## 5 f86f1ab4-1fb… A Single-Cell Trans… <chr [2]> <chr [1]> <chr [1]>
## 6 c1810dbc-16d… A cell atlas of hum… <chr [2]> <chr [2]> <chr [2]>
## 7 996120f9-e84… A human single cell… <chr [1]> <chr [1]> <chr [1]>
## 8 6072616c-879… A revised airway ep… <chr [1]> <chr [1]> <chr [1]>
## 9 d3446f0c-30f… A single cell atlas… <chr [0]> <chr [0]> <chr [0]>
## 10 842605c7-375… A single cell atlas… <chr [1]> <chr [1]> <chr [1]>
## # … with 114 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: 52 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 53c53cd4-812… A Cellular Anatomy … <chr [1]> <chr [1]> <chr [1]>
## 2 7027adc6-c9c… A Cellular Atlas of… <chr [1]> <chr [1]> <chr [1]>
## 3 c1810dbc-16d… A cell atlas of hum… <chr [2]> <chr [2]> <chr [2]>
## 4 996120f9-e84… A human single cell… <chr [1]> <chr [1]> <chr [1]>
## 5 842605c7-375… A single cell atlas… <chr [1]> <chr [1]> <chr [1]>
## 6 4a95101c-9ff… A single-cell refer… <chr [1]> <chr [4]> <chr [4]>
## 7 1cd1f41f-f81… A single-cell surve… <chr [1]> <chr [1]> <chr [1]>
## 8 8185730f-411… A single-cell trans… <chr [1]> <chr [1]> <chr [1]>
## 9 38449aea-70b… Altered human oligo… <chr [1]> <chr [1]> <chr [1]>
## 10 0fd8f918-62d… An Atlas of Immune … <chr [1]> <chr [1]> <chr [1]>
## # … with 42 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 "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"
## [,3]
## 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"
## [,4]
## projectId "2ef3655a-973d-4d69-9b41-21fa4041eed7"
## projectTitle "Single-cell RNA sequencing of normal human kidney"
## genusSpecies "Homo sapiens"
## samples.organ "kidney"
## specimens.organ "kidney"
## [,5]
## 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
## [,6]
## 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"
## [,7]
## 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"
## [,8]
## projectId "9d97f01f-9313-416e-9b07-560f048b2350"
## projectTitle "Single-cell RNA-sequencing of skin, fresh blood, and cultured peripheral blood mononuclear cells fr" [truncated]
## genusSpecies "Homo sapiens"
## samples.organ character,2
## specimens.organ character,2
## [,9]
## 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"
## [,10]
## 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"
## [,11]
## 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"
## [,12]
## 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"
## [,13]
## 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"
## [,14]
## 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 fe214fe… bone-ma… loom 4.04e7 2021-0… Single cell … 0c3b7785-… https:/…
## 2 e8136d6… 800cab7… loom 7.41e8 2021-0… Single cell … 0c3b7785-… https:/…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: 36 × 3
## facet n_terms n_values
## <chr> <int> <int>
## 1 assayType 1 124
## 2 biologicalSex 5 199
## 3 cellLineType 6 130
## 4 contactName 1066 1300
## 5 contentDescription 21 346
## 6 developmentStage 51 195
## 7 donorDisease 129 271
## 8 effectiveOrgan 70 190
## 9 fileFormat 25 403
## 10 fileSource 10 303
## # … with 26 more rowsNote the fileFormat facet, and repeat projects_facets() to
discover detail about available file formats
projects_facets("fileFormat")
## # A tibble: 25 × 3
## facet term count
## <chr> <chr> <int>
## 1 fileFormat fastq.gz 114
## 2 fileFormat bam 52
## 3 fileFormat loom 52
## 4 fileFormat tar 38
## 5 fileFormat csv 25
## 6 fileFormat txt.gz 22
## 7 fileFormat zip 13
## 8 fileFormat h5ad 10
## 9 fileFormat csv.gz 9
## 10 fileFormat pdf 9
## # … with 15 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: 10 × 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 c1810dbc-16d… A cell atlas of hum… <chr [2]> <chr [2]> <chr [2]>
## 2 ad98d3cd-26f… Cells of the adult … <chr [1]> <chr [1]> <chr [1]>
## 3 83f5188e-3bf… Distinct microbial … <chr [1]> <chr [2]> <chr [2]>
## 4 c4077b3c-5c9… Ischaemic sensitivi… <chr [1]> <chr [3]> <chr [3]>
## 5 091cf39b-01b… Profiling of CD34+ … <chr [1]> <chr [0]> <chr [1]>
## 6 f83165c5-e2e… Reconstructing the … <chr [1]> <chr [3]> <chr [3]>
## 7 abe1a013-af7… Spatio-temporal imm… <chr [1]> <chr [1]> <chr [1]>
## 8 b963bd4b-4bc… The cellular immune… <chr [1]> <chr [1]> <chr [1]>
## 9 4e6f083b-5b9… The emergent landsc… <chr [1]> <chr [3]> <chr [3]>
## 10 455b46e6-d8e… Transcriptomic char… <chr [1]> <chr [3]> <chr [3]>The default tibble produced by projects() contains only some of the
information available; the information is much richer.
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
## 124 8 37hits represents each project as a list, e.g,.
lengths(projects_list$hits[[1]])
## protocols entryId sources projects
## 2 1 1 1
## samples specimens cellLines donorOrganisms
## 1 1 0 1
## organoids cellSuspensions fileTypeSummaries
## 0 1 2shows that there are 10 different ways in which the first project is described. Each component is itself a list-of-lists, e.g.,
lengths(projects_list$hits[[1]]$projects[[1]])
## projectId projectTitle projectShortname
## 1 1 1
## laboratory projectDescription contributors
## 1 1 6
## publications arrayExpressAccessions geoSeriesAccessions
## 1 1 1
## insdcProjectAccessions insdcStudyAccessions supplementaryLinks
## 1 1 1
## matrices contributorMatrices accessible
## 0 1 1
projects_list$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: 4390
## # total number of elements: 48775
## # number of leaf paths: 3205
## # number of leaf elements: 34500
## # lol_path():
## # A tibble: 4,390 × 3
## path n is_leaf
## <chr> <int> <lgl>
## 1 hits 1 FALSE
## 2 hits[*] 124 FALSE
## 3 hits[*].cellLines 124 FALSE
## 4 hits[*].cellLines[*] 14 FALSE
## 5 hits[*].cellLines[*].cellLineType 14 FALSE
## 6 hits[*].cellLines[*].cellLineType[*] 20 TRUE
## 7 hits[*].cellLines[*].id 14 FALSE
## 8 hits[*].cellLines[*].id[*] 85 TRUE
## 9 hits[*].cellLines[*].modelOrgan 14 FALSE
## 10 hits[*].cellLines[*].modelOrgan[*] 25 TRUE
## # … with 4,380 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: 4272
## # total number of elements: 21514
## # number of leaf paths: 3151
## # number of leaf elements: 16436
## # lol_path():
## # A tibble: 4,272 × 3
## path n is_leaf
## <chr> <int> <lgl>
## 1 hits[*].projects[*] 124 FALSE
## 2 hits[*].projects[*].accessible 124 TRUE
## 3 hits[*].projects[*].arrayExpressAccessions 124 FALSE
## 4 hits[*].projects[*].arrayExpressAccessions[*] 130 TRUE
## 5 hits[*].projects[*].contributorMatrices 124 FALSE
## 6 hits[*].projects[*].contributorMatrices.developmentStage 4 FALSE
## 7 hits[*].projects[*].contributorMatrices.developmentStage.adult 4 FALSE
## 8 hits[*].projects[*].contributorMatrices.developmentStage.adult… 2 FALSE
## 9 hits[*].projects[*].contributorMatrices.developmentStage.adult… 1 FALSE
## 10 hits[*].projects[*].contributorMatrices.developmentStage.adult… 1 FALSE
## # … with 4,262 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] 124
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: 10 × 6
## projectId projectTitle genusSpecies donorCount cellSuspensions… totalCells
## <chr> <chr> <list> <int> <list> <list>
## 1 c1810dbc-… A cell atlas … <chr [2]> 24 <chr [2]> <int [2]>
## 2 ad98d3cd-… Cells of the … <chr [1]> 14 <chr [1]> <int [1]>
## 3 83f5188e-… Distinct micr… <chr [1]> 6 <chr [2]> <int [2]>
## 4 c4077b3c-… Ischaemic sen… <chr [1]> 14 <chr [3]> <int [3]>
## 5 091cf39b-… Profiling of … <chr [1]> 3 <chr [1]> <int [1]>
## 6 f83165c5-… Reconstructin… <chr [1]> 16 <chr [3]> <int [0]>
## 7 abe1a013-… Spatio-tempor… <chr [1]> 8 <chr [1]> <int [0]>
## 8 b963bd4b-… The cellular … <chr [1]> 120 <chr [1]> <int [1]>
## 9 4e6f083b-… The emergent … <chr [1]> 6 <chr [3]> <int [3]>
## 10 455b46e6-… Transcriptomi… <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: 10 × 3
## projectId cellSuspensions.organ totalCells
## <chr> <list> <list>
## 1 c1810dbc-16d2-45c3-b45e-3e675f88d87b <chr [2]> <int [2]>
## 2 ad98d3cd-26fb-4ee3-99c9-8a2ab085e737 <chr [1]> <int [1]>
## 3 83f5188e-3bf7-4956-9544-cea4f8997756 <chr [2]> <int [2]>
## 4 c4077b3c-5c98-4d26-a614-246d12c2e5d7 <chr [3]> <int [3]>
## 5 091cf39b-01bc-42e5-9437-f419a66c8a45 <chr [1]> <int [1]>
## 6 f83165c5-e2ea-4d15-a5cf-33f3550bffde <chr [3]> <int [0]>
## 7 abe1a013-af7a-45ed-8c26-f3793c24a1f4 <chr [1]> <int [0]>
## 8 b963bd4b-4bc1-4404-8425-69d74bc636b8 <chr [1]> <int [1]>
## 9 4e6f083b-5b9a-4393-9890-2a83da8188f1 <chr [3]> <int [3]>
## 10 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 presumptive gut 30952
## 12 4e6f083b-5b9a-4393-9890-2a83da8188f1 endoderm 54166
## 13 4e6f083b-5b9a-4393-9890-2a83da8188f1 embryo 27083
## 14 455b46e6-d8ea-4611-861e-de720a562ada bone marrow 87532
## 15 455b46e6-d8ea-4611-861e-de720a562ada blood 25016
## 16 455b46e6-d8ea-4611-861e-de720a562ada spleen 60043Select 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=dcp7&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-e2e… Reconstructing the h… <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/2702d06362079e_2702d06362079e.csv"
## d04c6e3c-b740-5586-8420-4480a1b5706c-2021-02-10T16:56:40.419579Z
## "/home/biocbuild/.cache/R/hca/2702d036ed90a2_2702d036ed90a2.csv"
## d30ffc0b-7d6e-5b85-aff9-21ec69663a81-2021-02-10T16:56:40.419579Z
## "/home/biocbuild/.cache/R/hca/2702d0686bf175_2702d0686bf175.csv"
## e1517725-01b0-5346-9788-afca63e9993a-2021-02-10T16:56:40.419579Z
## "/home/biocbuild/.cache/R/hca/2702d0208cf3d_2702d0208cf3d.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 74b6d569-3b1… 1.3 Million Brain C… <chr [1]> <chr [1]> <chr [1]>
## 2 53c53cd4-812… A Cellular Anatomy … <chr [1]> <chr [1]> <chr [1]>
## 3 7027adc6-c9c… A Cellular Atlas of… <chr [1]> <chr [1]> <chr [1]>
## 4 60ea42e1-af4… A Protocol for Reve… <chr [1]> <chr [1]> <chr [1]>
## 5 f86f1ab4-1fb… A Single-Cell Trans… <chr [2]> <chr [1]> <chr [1]>
## 6 c1810dbc-16d… A cell atlas of hum… <chr [2]> <chr [2]> <chr [2]>
## 7 996120f9-e84… A human single cell… <chr [1]> <chr [1]> <chr [1]>
## 8 6072616c-879… A revised airway ep… <chr [1]> <chr [1]> <chr [1]>
## 9 d3446f0c-30f… A single cell atlas… <chr [0]> <chr [0]> <chr [0]>
## 10 842605c7-375… A single cell atlas… <chr [1]> <chr [1]> <chr [1]>
## # … 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 8a40ff19-e61… Dissecting the Glob… <chr [1]> <chr [1]> <chr [1]>
## 2 ccef38d7-aa9… Dissecting the clon… <chr [2]> <chr [5]> <chr [5]>
## 3 4d6f6c96-2a8… Dissecting the huma… <chr [1]> <chr [1]> <chr [1]>
## 4 efea6426-510… Dissecting the prot… <chr [1]> <chr [1]> <chr [1]>
## 5 83f5188e-3bf… Distinct microbial … <chr [1]> <chr [2]> <chr [2]>
## 6 3e329187-a9c… Establishing Cerebr… <chr [1]> <chr [0]> <chr [2]>
## 7 41fb1734-a12… GM-CSF-producing T … <chr [1]> <chr [1]> <chr [1]>
## 8 52d10a60-c8d… Genomic profiling o… <chr [1]> <chr [1]> <chr [1]>
## 9 0d4b87ea-6e9… High throughput err… <chr [1]> <chr [1]> <chr [1]>
## 10 d2111fac-3fc… Human cerebral orga… <chr [1]> <chr [1]> <chr [3]>
## # … 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 74b6d569-3b1… 1.3 Million Brain C… <chr [1]> <chr [1]> <chr [1]>
## 2 53c53cd4-812… A Cellular Anatomy … <chr [1]> <chr [1]> <chr [1]>
## 3 7027adc6-c9c… A Cellular Atlas of… <chr [1]> <chr [1]> <chr [1]>
## 4 60ea42e1-af4… A Protocol for Reve… <chr [1]> <chr [1]> <chr [1]>
## 5 f86f1ab4-1fb… A Single-Cell Trans… <chr [2]> <chr [1]> <chr [1]>
## 6 c1810dbc-16d… A cell atlas of hum… <chr [2]> <chr [2]> <chr [2]>
## 7 996120f9-e84… A human single cell… <chr [1]> <chr [1]> <chr [1]>
## 8 6072616c-879… A revised airway ep… <chr [1]> <chr [1]> <chr [1]>
## 9 d3446f0c-30f… A single cell atlas… <chr [0]> <chr [0]> <chr [0]>
## 10 842605c7-375… A single cell atlas… <chr [1]> <chr [1]> <chr [1]>
## # … 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 Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure"
page_2_lol <-
page_1_lol %>%
hca_next()
page_2_lol %>%
lol_pull("hits[*].projects[*].projectTitle")
## [1] "A cell atlas of human thymic development defines T cell repertoire formation"
## [2] "A human single cell atlas of the substantia nigra reveals novel cell specific pathways associated with the genetic risk of Parkinson’s disease and neuropsychiatric disorders."
## [3] "A revised airway epithelial hierarchy includes CFTR-expressing ionocytes"
## [4] "A single cell atlas of human teeth"
## [5] "A single cell atlas of the human proximal epididymis reveals cell-type specific functions and distinct roles for CFTR."
## 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 Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure"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 × 8
## entryId projectTitle genusSpecies samples.organ disease instrumentManuf…
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 012c52ff-… A Cellular Atl… Mus musculus heart normal Illumina NextSe…
## 2 035db5b9-… A Cellular Atl… Mus musculus heart normal Illumina NextSe…
## 3 09e425f7-… A Cellular Atl… Mus musculus heart normal Illumina NextSe…
## 4 2273e44d-… A Cellular Atl… Mus musculus heart normal Illumina NextSe…
## # … with 2 more variables: fileType <chr>, count <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 o… Mus musculus <chr [2… <chr… 0d391bd1-92a9… 2021-02-26T01:…
## 2 A Cellular Atlas o… Mus musculus <chr [1… <chr… 165a2df1-07a0… 2021-02-26T01:…
## 3 A Cellular Atlas o… Mus musculus <chr [2… <chr… 166c1b1a-ad9c… 2020-08-04T10:…
## 4 A Cellular Atlas o… Mus musculus <chr [1… <chr… 18bad6b1-c55d… 2021-02-26T01:…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: 4 × 3
## fileType count totalSize
## <chr> <int> <dbl>
## 1 fastq.gz 28219 4616483104138
## 2 loom 168 323739761632
## 3 bam 164 3284598129743
## 4 Rds 3 2637887113
first_catalog <- catalogs()[1]
summary(type = "overview", catalog = first_catalog)
## # A tibble: 8 × 2
## name value
## <chr> <dbl>
## 1 totalFileSize 8.99e13
## 2 fileCount 3.50e 5
## 3 donorCount 1.32e 3
## 4 specimenCount 8.06e 3
## 5 speciesCount 3 e 0
## 6 projectCount 1.24e 2
## 7 labCount 2.81e 2
## 8 totalCellCount 1.37e 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-c9c… A Cellular Atlas of … Mus musculus <chr [1]> <chr [1]>
## 2 ad98d3cd-26f… Cells of the adult h… Homo sapiens <chr [1]> <chr [1]>
## 3 bd400331-54b… Sex-Specific Control… Homo sapiens <chr [1]> <chr [1]>
## 4 e0009214-c0a… Tabula Muris: Transc… Mus musculus <chr [18]> <chr [18]>
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] "08755a99-c8f0-420a-9d21-4dca10b40ba5"
##
## $sources[[1]]$sourceSpec
## [1] "tdr:broad-datarepo-terra-prod-hca2:snapshot/hca_prod_20201120_dcp2___20210707_dcp7:"
##
##
##
## $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"
##
##
## $projects[[1]]$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] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[1]]$contactName
## [1] "Catherine,L.,Worth"
##
## $projects[[1]]$contributors[[1]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[1]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[1]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[1]]$email
## [1] "catherine.sargent@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[2]]
## $projects[[1]]$contributors[[2]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[2]]$contactName
## [1] "Daniel,,DeLaughter"
##
## $projects[[1]]$contributors[[2]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[2]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[2]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[2]]$email
## [1] "Daniel_DeLaughter@hms.harvard.edu"
##
##
## $projects[[1]]$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] "Brigham and Women’s Hospital"
##
## $projects[[1]]$contributors[[4]]$contactName
## [1] "Barbara,,McDonough"
##
## $projects[[1]]$contributors[[4]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[4]]$laboratory
## [1] "Cardiovascular Division"
##
## $projects[[1]]$contributors[[4]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[4]]$email
## [1] "mcdonough@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[5]]
## $projects[[1]]$contributors[[5]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[5]]$contactName
## [1] "Kenny,,Roberts"
##
## $projects[[1]]$contributors[[5]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[5]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[5]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[5]]$email
## [1] "kr19@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[6]]
## $projects[[1]]$contributors[[6]]$institution
## [1] "Sun-Yat Sen University"
##
## $projects[[1]]$contributors[[6]]$contactName
## [1] "Hongbo,,Zhang"
##
## $projects[[1]]$contributors[[6]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[6]]$laboratory
## [1] "Department of Histology and Embryology of Zhongshan School of Medicine"
##
## $projects[[1]]$contributors[[6]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[6]]$email
## [1] "hz3@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[7]]
## $projects[[1]]$contributors[[7]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[7]]$contactName
## [1] "Christine,,Seidman"
##
## $projects[[1]]$contributors[[7]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[7]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[7]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[7]]$email
## [1] "cseidman@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[8]]
## $projects[[1]]$contributors[[8]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[8]]$contactName
## [1] "Eirini,S.,Fasouli"
##
## $projects[[1]]$contributors[[8]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[8]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[8]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[8]]$email
## [1] "ef5@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[9]]
## $projects[[1]]$contributors[[9]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[9]]$contactName
## [1] "Hiroko,,Wakimoto"
##
## $projects[[1]]$contributors[[9]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[9]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[9]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[9]]$email
## [1] "hwakimoto@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[10]]
## $projects[[1]]$contributors[[10]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[10]]$contactName
## [1] "Liz,,Tuck"
##
## $projects[[1]]$contributors[[10]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[10]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[10]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[10]]$email
## [1] "et2@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[11]]
## $projects[[1]]$contributors[[11]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[11]]$contactName
## [1] "Joseph,J.,Boyle"
##
## $projects[[1]]$contributors[[11]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[11]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[11]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[11]]$email
## [1] "joseph.boyle@imperial.ac.uk"
##
##
## $projects[[1]]$contributors[[12]]
## $projects[[1]]$contributors[[12]]$institution
## [1] "University of Alberta"
##
## $projects[[1]]$contributors[[12]]$contactName
## [1] "Anissa,,Viveiros"
##
## $projects[[1]]$contributors[[12]]$projectRole
## [1] "biomaterial provider"
##
## $projects[[1]]$contributors[[12]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
##
## $projects[[1]]$contributors[[12]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[12]]$email
## [1] "aviveiro@ualberta.ca"
##
##
## $projects[[1]]$contributors[[13]]
## $projects[[1]]$contributors[[13]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[13]]$contactName
## [1] "Michael,,Lee"
##
## $projects[[1]]$contributors[[13]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[13]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[13]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[13]]$email
## [1] "michael.lee@imperial.ac.uk"
##
##
## $projects[[1]]$contributors[[14]]
## $projects[[1]]$contributors[[14]]$institution
## [1] "Cambridge Biorepository for Translational Medicine"
##
## $projects[[1]]$contributors[[14]]$contactName
## [1] "Kourosh,,Saeb-Parsy"
##
## $projects[[1]]$contributors[[14]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[14]]$laboratory
## NULL
##
## $projects[[1]]$contributors[[14]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[14]]$email
## [1] "ks10014@cam.ac.uk"
##
##
## $projects[[1]]$contributors[[15]]
## $projects[[1]]$contributors[[15]]$institution
## [1] "Cambridge Biorepository for Translational Medicine"
##
## $projects[[1]]$contributors[[15]]$contactName
## [1] "Krishnaa,T.,Mahbubani"
##
## $projects[[1]]$contributors[[15]]$projectRole
## [1] "biomaterial provider"
##
## $projects[[1]]$contributors[[15]]$laboratory
## NULL
##
## $projects[[1]]$contributors[[15]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[15]]$email
## [1] "ktam2@cam.ac.uk"
##
##
## $projects[[1]]$contributors[[16]]
## $projects[[1]]$contributors[[16]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[16]]$contactName
## [1] "Sara,,Samari"
##
## $projects[[1]]$contributors[[16]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[16]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[16]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[16]]$email
## [1] "sara.samari13@imperial.ac.uk"
##
##
## $projects[[1]]$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] "Eric,L.,Lindberg"
##
## $projects[[1]]$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] "Eric.Lindberg@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[18]]
## $projects[[1]]$contributors[[18]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[18]]$contactName
## [1] "Carlos,,Talavera-López"
##
## $projects[[1]]$contributors[[18]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[18]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[18]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[18]]$email
## [1] "ct5@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[19]]
## $projects[[1]]$contributors[[19]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[19]]$contactName
## [1] "Omer,,Bayraktar"
##
## $projects[[1]]$contributors[[19]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[19]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[19]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[19]]$email
## [1] "ob5@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[20]]
## $projects[[1]]$contributors[[20]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[20]]$contactName
## [1] "Masatoshi,,Kanda"
##
## $projects[[1]]$contributors[[20]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[20]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[20]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[20]]$email
## [1] "masatoshi.kanda@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[21]]
## $projects[[1]]$contributors[[21]]$institution
## [1] "University of Alberta"
##
## $projects[[1]]$contributors[[21]]$contactName
## [1] "Gavin,,Oudit"
##
## $projects[[1]]$contributors[[21]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[21]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
##
## $projects[[1]]$contributors[[21]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[21]]$email
## [1] "gavin.oudit@ualberta.ca"
##
##
## $projects[[1]]$contributors[[22]]
## $projects[[1]]$contributors[[22]]$institution
## [1] "University of Alberta"
##
## $projects[[1]]$contributors[[22]]$contactName
## [1] "Hao,,Zhang"
##
## $projects[[1]]$contributors[[22]]$projectRole
## [1] "biomaterial provider"
##
## $projects[[1]]$contributors[[22]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
##
## $projects[[1]]$contributors[[22]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[22]]$email
## [1] "hzhang10@ualberta.ca"
##
##
## $projects[[1]]$contributors[[23]]
## $projects[[1]]$contributors[[23]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[23]]$contactName
## [1] "J.,G.,Seidman"
##
## $projects[[1]]$contributors[[23]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[23]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[23]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[23]]$email
## [1] "seidman@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[24]]
## $projects[[1]]$contributors[[24]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[24]]$contactName
## [1] "Michela,,Noseda"
##
## $projects[[1]]$contributors[[24]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[24]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[24]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[24]]$email
## [1] "m.noseda@imperial.ac.uk"
##
##
## $projects[[1]]$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] "Giannino,,Patone"
##
## $projects[[1]]$contributors[[26]]$projectRole
## [1] "computational scientist"
##
## $projects[[1]]$contributors[[26]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[26]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[26]]$email
## [1] "Giannino.Patone@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[27]]
## $projects[[1]]$contributors[[27]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[27]]$contactName
## [1] "Krzysztof,,Polanski"
##
## $projects[[1]]$contributors[[27]]$projectRole
## [1] "computational scientist"
##
## $projects[[1]]$contributors[[27]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[27]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[27]]$email
## [1] "kp9@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[28]]
## $projects[[1]]$contributors[[28]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[28]]$contactName
## [1] "Norbert,,Hübner"
##
## $projects[[1]]$contributors[[28]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[28]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[28]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[28]]$email
## [1] "nhuebner@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[29]]
## $projects[[1]]$contributors[[29]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[29]]$contactName
## [1] "Henrike,,Maatz"
##
## $projects[[1]]$contributors[[29]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[29]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[29]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[29]]$email
## [1] "h.maatz@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[30]]
## $projects[[1]]$contributors[[30]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[30]]$contactName
## [1] "Monika,,Litviňuková"
##
## $projects[[1]]$contributors[[30]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[30]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[30]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[30]]$email
## [1] "monika.litvinukova@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[31]]
## $projects[[1]]$contributors[[31]]$institution
## [1] "HMGU"
##
## $projects[[1]]$contributors[[31]]$contactName
## [1] "Matthias,,Heinig"
##
## $projects[[1]]$contributors[[31]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[31]]$laboratory
## [1] "Institute of Computational Biology (ICB)"
##
## $projects[[1]]$contributors[[31]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[31]]$email
## [1] "matthias.heinig@helmholtz-muenchen.de"
##
##
## $projects[[1]]$contributors[[32]]
## $projects[[1]]$contributors[[32]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[32]]$contactName
## [1] "Joshua,M,Gorham"
##
## $projects[[1]]$contributors[[32]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[32]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[32]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[32]]$email
## [1] "jgorham@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[33]]
## $projects[[1]]$contributors[[33]]$institution
## [1] "EMBL-EBI"
##
## $projects[[1]]$contributors[[33]]$contactName
## [1] "Marion,F,Shadbolt"
##
## $projects[[1]]$contributors[[33]]$projectRole
## [1] "data curator"
##
## $projects[[1]]$contributors[[33]]$laboratory
## [1] "Human Cell Atlas Data Coordination Platform"
##
## $projects[[1]]$contributors[[33]]$correspondingContributor
## [1] FALSE
##
## $projects[[1]]$contributors[[33]]$email
## [1] "mshadbolt@ebi.ac.uk"
##
##
## $projects[[1]]$contributors[[34]]
## $projects[[1]]$contributors[[34]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[34]]$contactName
## [1] "Sarah,A.,Teichmann"
##
## $projects[[1]]$contributors[[34]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[34]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[34]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[34]]$email
## [1] "st9@sanger.ac.uk"
##
##
##
## $projects[[1]]$publications
## $projects[[1]]$publications[[1]]
## $projects[[1]]$publications[[1]]$publicationTitle
## [1] "Cells of the adult human heart"
##
## $projects[[1]]$publications[[1]]$publicationUrl
## [1] "https://www.nature.com/articles/s41586-020-2797-4"
##
##
##
## $projects[[1]]$arrayExpressAccessions
## $projects[[1]]$arrayExpressAccessions[[1]]
## NULL
##
##
## $projects[[1]]$geoSeriesAccessions
## $projects[[1]]$geoSeriesAccessions[[1]]
## NULL
##
##
## $projects[[1]]$insdcProjectAccessions
## $projects[[1]]$insdcProjectAccessions[[1]]
## [1] "ERP123138"
##
##
## $projects[[1]]$insdcStudyAccessions
## $projects[[1]]$insdcStudyAccessions[[1]]
## [1] "PRJEB39602"
##
##
## $projects[[1]]$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]]$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]]$name
## [1] "human-heart-10XV3.loom"
##
## $projects[[1]]$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]]$matrixCellCount
## NULL
##
## $projects[[1]]$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]]$matrix_cell_count
## NULL
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$source
## [1] "DCP/2 Analysis"
##
## $projects[[1]]$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=dcp7&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]]$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]]$name
## [1] "human-heart-10XV2.loom"
##
## $projects[[1]]$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]]$matrixCellCount
## NULL
##
## $projects[[1]]$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]]$matrix_cell_count
## NULL
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$source
## [1] "DCP/2 Analysis"
##
## $projects[[1]]$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=dcp7&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]]$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]]$name
## [1] "human-heart-10XV2.loom"
##
## $projects[[1]]$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]]$matrixCellCount
## NULL
##
## $projects[[1]]$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]]$matrix_cell_count
## NULL
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$source
## [1] "DCP/2 Analysis"
##
## $projects[[1]]$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=dcp7&version=2021-02-15T14%3A15%3A05.000000Z"
##
##
##
##
##
##
##
##
##
##
##
## $projects[[1]]$contributorMatrices
## $projects[[1]]$contributorMatrices$genusSpecies
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "b30d1a16-fb04-5ac7-999f-6ce9d1de0c76"
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-10T17:01:03.177554Z"
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$name
## [1] "hca_heart_global_ctl200723_freeze.h5ad"
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$size
## [1] 5068859764
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrixCellCount
## NULL
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$fileSource
## [1] "Contributor"
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrix_cell_count
## NULL
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$source
## [1] "Contributor"
##
## $projects[[1]]$contributorMatrices$genusSpecies$`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=dcp7&version=2021-02-10T17%3A01%3A03.177554Z"
##
##
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$uuid
## [1] "b30d1a16-fb04-5ac7-999f-6ce9d1de0c76"
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$version
## [1] "2021-02-10T17:01:03.177554Z"
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$name
## [1] "hca_heart_global_ctl200723_freeze.h5ad"
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$size
## [1] 5068859764
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$matrixCellCount
## NULL
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$fileSource
## [1] "Contributor"
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$matrix_cell_count
## NULL
##
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$source
## [1] "Contributor"
##
## $projects[[1]]$contributorMatrices$genusSpecies$`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=dcp7&version=2021-02-10T17%3A01%3A03.177554Z"
##
##
##
##
##
##
##
##
##
##
##
## $projects[[1]]$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
##
##
##
## $fileTypeSummaries
## $fileTypeSummaries[[1]]
## $fileTypeSummaries[[1]]$format
## [1] "fastq.gz"
##
## $fileTypeSummaries[[1]]$fileType
## [1] "fastq.gz"
##
## $fileTypeSummaries[[1]]$fileSource
## $fileTypeSummaries[[1]]$fileSource[[1]]
## NULL
##
##
## $fileTypeSummaries[[1]]$source
## $fileTypeSummaries[[1]]$source[[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"
##
## $fileTypeSummaries[[2]]$fileType
## [1] "loom"
##
## $fileTypeSummaries[[2]]$fileSource
## $fileTypeSummaries[[2]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
##
##
## $fileTypeSummaries[[2]]$source
## $fileTypeSummaries[[2]]$source[[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"
##
## $fileTypeSummaries[[3]]$fileType
## [1] "bam"
##
## $fileTypeSummaries[[3]]$fileSource
## $fileTypeSummaries[[3]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
##
##
## $fileTypeSummaries[[3]]$source
## $fileTypeSummaries[[3]]$source[[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] "h5ad"
##
## $fileTypeSummaries[[4]]$fileType
## [1] "h5ad"
##
## $fileTypeSummaries[[4]]$fileSource
## $fileTypeSummaries[[4]]$fileSource[[1]]
## [1] "Contributor"
##
##
## $fileTypeSummaries[[4]]$source
## $fileTypeSummaries[[4]]$source[[1]]
## [1] "Contributor"
##
##
## $fileTypeSummaries[[4]]$count
## [1] 1
##
## $fileTypeSummaries[[4]]$totalSize
## [1] 5068859764
##
## $fileTypeSummaries[[4]]$matrixCellCount
## NULL
##
## $fileTypeSummaries[[4]]$isIntermediate
## [1] FALSE
##
## $fileTypeSummaries[[4]]$contentDescription
## $fileTypeSummaries[[4]]$contentDescription[[1]]
## [1] "Matrix"
##
##
##
## $fileTypeSummaries[[5]]
## $fileTypeSummaries[[5]]$format
## [1] "loom"
##
## $fileTypeSummaries[[5]]$fileType
## [1] "loom"
##
## $fileTypeSummaries[[5]]$fileSource
## $fileTypeSummaries[[5]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
##
##
## $fileTypeSummaries[[5]]$source
## $fileTypeSummaries[[5]]$source[[1]]
## [1] "DCP/2 Analysis"
##
##
## $fileTypeSummaries[[5]]$count
## [1] 2
##
## $fileTypeSummaries[[5]]$totalSize
## [1] 7653912940
##
## $fileTypeSummaries[[5]]$matrixCellCount
## NULL
##
## $fileTypeSummaries[[5]]$isIntermediate
## [1] FALSE
##
## $fileTypeSummaries[[5]]$contentDescription
## $fileTypeSummaries[[5]]$contentDescription[[1]]
## [1] "Count Matrix"sessionInfo()
## R version 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-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] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] hca_1.0.3 LoomExperiment_1.10.1
## [3] BiocIO_1.2.0 rhdf5_2.36.0
## [5] SingleCellExperiment_1.14.1 SummarizedExperiment_1.22.0
## [7] Biobase_2.52.0 GenomicRanges_1.44.0
## [9] GenomeInfoDb_1.28.1 IRanges_2.26.0
## [11] MatrixGenerics_1.4.2 matrixStats_0.60.0
## [13] S4Vectors_0.30.0 BiocGenerics_0.38.0
## [15] dplyr_1.0.7 httr_1.4.2
## [17] BiocStyle_2.20.2
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.0 tidyr_1.1.3 bit64_4.0.5
## [4] jsonlite_1.7.2 bslib_0.2.5.1 assertthat_0.2.1
## [7] BiocManager_1.30.16 BiocFileCache_2.0.0 blob_1.2.2
## [10] GenomeInfoDbData_1.2.6 yaml_2.2.1 pillar_1.6.2
## [13] RSQLite_2.2.8 lattice_0.20-44 glue_1.4.2
## [16] digest_0.6.27 XVector_0.32.0 htmltools_0.5.1.1
## [19] Matrix_1.3-4 pkgconfig_2.0.3 bookdown_0.23
## [22] zlibbioc_1.38.0 purrr_0.3.4 HDF5Array_1.20.0
## [25] tibble_3.1.3 generics_0.1.0 ellipsis_0.3.2
## [28] withr_2.4.2 cachem_1.0.6 cli_3.0.1
## [31] magrittr_2.0.1 crayon_1.4.1 memoise_2.0.0
## [34] evaluate_0.14 fansi_0.5.0 tools_4.1.0
## [37] lifecycle_1.0.0 stringr_1.4.0 Rhdf5lib_1.14.2
## [40] DelayedArray_0.18.0 compiler_4.1.0 jquerylib_0.1.4
## [43] rlang_0.4.11 grid_4.1.0 RCurl_1.98-1.4
## [46] rhdf5filters_1.4.0 rappdirs_0.3.3 bitops_1.0-7
## [49] rmarkdown_2.10 DBI_1.1.1 curl_4.3.2
## [52] R6_2.5.1 knitr_1.33 fastmap_1.1.0
## [55] bit_4.0.4 utf8_1.2.2 filelock_1.0.2
## [58] stringi_1.7.3 Rcpp_1.0.7 vctrs_0.3.8
## [61] dbplyr_2.1.1 tidyselect_1.1.1 xfun_0.25