The purpose of this vignette is to explore the file manifests available from the Human Cell Atlas project.
These files provide a metadata summary for a collection of files in a tabular format, including but not limited to information about process and workflow used to generate the file, information about the specimens the file data were derived from, and identifiers connect specific projects, files, and specimens.
The WARP (WDL Analysis Research Pipelines) repository contains information on a variety of pipelines, and can be used alongside a manifest to better understand the metadata.
Evaluate the following code chunk to install packages required for this vignette.
## install from Bioconductor if you haven't already
pkgs <- c("LoomExperiment", "hca")
pkgs_needed <- pkgs[!pkgs %in% rownames(installed.packages())]
BiocManager::install(pkgs_needed)Load the packages into your R session.
library(dplyr)
library(SummarizedExperiment)
library(LoomExperiment)
library(hca)default_manifest_tbl <- hca::manifest()
## requesting manifest
default_manifest_tbl
## # A tibble: 358,176 x 55
## source_id source_spec bundle_uuid bundle_version file_document_id
## <chr> <chr> <chr> <dttm> <chr>
## 1 cf3cfc49-d~ tdr:tdr-fp-54~ ffed96bd-be~ 2021-05-14 13:58:58 0000591a-0df3-40~
## 2 cf3cfc49-d~ tdr:tdr-fp-54~ 4ef10b20-d5~ 2019-08-01 20:01:47 0000c13f-a299-48~
## 3 cf3cfc49-d~ tdr:tdr-fp-54~ 0d43b1a9-71~ 2019-05-17 16:05:38 0001010d-8f9a-41~
## 4 cf3cfc49-d~ tdr:tdr-fp-54~ 2fb448ac-38~ 2021-02-25 20:02:24 00014fc3-7451-43~
## 5 cf3cfc49-d~ tdr:tdr-fp-54~ 2a61bc39-23~ 2019-08-01 20:01:47 0001614e-b44f-46~
## 6 cf3cfc49-d~ tdr:tdr-fp-54~ 17eb537d-b9~ 2019-05-16 21:18:13 00016bff-87d4-47~
## 7 cf3cfc49-d~ tdr:tdr-fp-54~ 894980d6-f3~ 2021-06-10 09:50:55 00016dd1-216e-4b~
## 8 cf3cfc49-d~ tdr:tdr-fp-54~ 0678bd67-ff~ 2019-08-01 20:01:47 000183e4-19f4-43~
## 9 cf3cfc49-d~ tdr:tdr-fp-54~ aa7364b0-c4~ 2021-05-14 13:58:53 000189b0-671a-45~
## 10 cf3cfc49-d~ tdr:tdr-fp-54~ 2d556dfb-0f~ 2019-08-01 20:01:46 0001b474-e38d-49~
## # ... with 358,166 more rows, and 50 more variables: file_type <chr>,
## # file_name <chr>, file_format <chr>, read_index <chr>, file_size <dbl>,
## # file_uuid <chr>, file_version <dttm>, file_crc32c <chr>, file_sha256 <chr>,
## # file_content_type <chr>, file_drs_uri <chr>, file_url <chr>,
## # cell_suspension.provenance.document_id <chr>,
## # cell_suspension.biomaterial_core.biomaterial_id <chr>,
## # cell_suspension.estimated_cell_count <dbl>, ...manifest_filter <- hca::filters(
projectId = list(is = "4a95101c-9ffc-4f30-a809-f04518a23803"),
fileFormat = list(is = "loom"),
workflow = list(is = c("optimus_v4.2.2", "optimus_v4.2.3"))
)
manifest_tibble <- hca::manifest(filters = manifest_filter)
## requesting manifest
manifest_tibble
## # A tibble: 20 x 55
## source_id source_spec bundle_uuid bundle_version file_document_id
## <chr> <chr> <chr> <dttm> <chr>
## 1 cf3cfc49-d~ tdr:tdr-fp-54~ b593b66a-d2~ 2020-02-03 01:00:00 131ea511-25f7-58~
## 2 cf3cfc49-d~ tdr:tdr-fp-54~ 5a63dd0b-52~ 2021-02-02 23:50:00 1bb375a5-d22b-59~
## 3 cf3cfc49-d~ tdr:tdr-fp-54~ 40733888-3b~ 2021-02-02 23:55:00 1f8ff0fa-6892-5e~
## 4 cf3cfc49-d~ tdr:tdr-fp-54~ 1a41ebe6-ee~ 2021-02-02 23:50:00 2fffe225-ba6c-59~
## 5 cf3cfc49-d~ tdr:tdr-fp-54~ c12a6ca2-32~ 2021-02-02 23:50:00 31aa5a18-2a4e-54~
## 6 cf3cfc49-d~ tdr:tdr-fp-54~ f58d690c-bb~ 2021-02-02 23:50:00 48eea299-8823-5a~
## 7 cf3cfc49-d~ tdr:tdr-fp-54~ 21c4e2de-ec~ 2021-02-02 23:50:00 51458973-404c-58~
## 8 cf3cfc49-d~ tdr:tdr-fp-54~ 50620c50-23~ 2021-02-02 23:50:00 5bbebef4-9b14-50~
## 9 cf3cfc49-d~ tdr:tdr-fp-54~ e3ecdfc2-44~ 2021-02-02 23:55:00 5bc232f2-b77c-52~
## 10 cf3cfc49-d~ tdr:tdr-fp-54~ ae338c4e-65~ 2021-02-02 23:50:00 6326b602-0f63-54~
## 11 cf3cfc49-d~ tdr:tdr-fp-54~ d62c4599-47~ 2020-02-03 01:00:00 7848d80b-6b1d-56~
## 12 cf3cfc49-d~ tdr:tdr-fp-54~ 81df106e-e7~ 2021-02-02 23:55:00 9f8bc032-6276-57~
## 13 cf3cfc49-d~ tdr:tdr-fp-54~ 2838323c-cd~ 2020-02-03 01:00:00 b98cfaac-64f5-59~
## 14 cf3cfc49-d~ tdr:tdr-fp-54~ c3f672ad-e6~ 2021-02-02 23:50:00 bf7751ae-ac9d-5b~
## 15 cf3cfc49-d~ tdr:tdr-fp-54~ a9c90392-ca~ 2020-02-03 01:00:00 c7b6470c-e2f0-51~
## 16 cf3cfc49-d~ tdr:tdr-fp-54~ 9d0f5cd1-0e~ 2020-02-03 01:00:00 d0b95f2c-98ae-58~
## 17 cf3cfc49-d~ tdr:tdr-fp-54~ 59de15e1-f5~ 2021-02-02 23:50:00 d18759a6-2a95-5d~
## 18 cf3cfc49-d~ tdr:tdr-fp-54~ 54fb0e25-57~ 2021-02-02 23:55:00 dfd9905b-d6c9-5a~
## 19 cf3cfc49-d~ tdr:tdr-fp-54~ 7516565a-e8~ 2021-02-02 23:55:00 e07ca731-b20a-5b~
## 20 cf3cfc49-d~ tdr:tdr-fp-54~ 8e850d2d-0b~ 2021-02-02 23:50:00 fd41f3d6-7664-53~
## # ... with 50 more variables: file_type <chr>, file_name <chr>,
## # file_format <chr>, read_index <lgl>, file_size <dbl>, file_uuid <chr>,
## # file_version <dttm>, file_crc32c <chr>, file_sha256 <chr>,
## # file_content_type <chr>, file_drs_uri <chr>, file_url <chr>,
## # cell_suspension.provenance.document_id <chr>,
## # cell_suspension.biomaterial_core.biomaterial_id <chr>,
## # cell_suspension.estimated_cell_count <lgl>, ...
## what specimen organs are represented in these files?
manifest_tibble |>
dplyr::count(specimen_from_organism.organ)
## # A tibble: 4 x 2
## specimen_from_organism.organ n
## <chr> <int>
## 1 blood 5
## 2 hematopoietic system 5
## 3 lung 5
## 4 mediastinal lymph node 5manifest_tibble and select one for downloadmanifest_tibble
## # A tibble: 20 x 55
## source_id source_spec bundle_uuid bundle_version file_document_id
## <chr> <chr> <chr> <dttm> <chr>
## 1 cf3cfc49-d~ tdr:tdr-fp-54~ b593b66a-d2~ 2020-02-03 01:00:00 131ea511-25f7-58~
## 2 cf3cfc49-d~ tdr:tdr-fp-54~ 5a63dd0b-52~ 2021-02-02 23:50:00 1bb375a5-d22b-59~
## 3 cf3cfc49-d~ tdr:tdr-fp-54~ 40733888-3b~ 2021-02-02 23:55:00 1f8ff0fa-6892-5e~
## 4 cf3cfc49-d~ tdr:tdr-fp-54~ 1a41ebe6-ee~ 2021-02-02 23:50:00 2fffe225-ba6c-59~
## 5 cf3cfc49-d~ tdr:tdr-fp-54~ c12a6ca2-32~ 2021-02-02 23:50:00 31aa5a18-2a4e-54~
## 6 cf3cfc49-d~ tdr:tdr-fp-54~ f58d690c-bb~ 2021-02-02 23:50:00 48eea299-8823-5a~
## 7 cf3cfc49-d~ tdr:tdr-fp-54~ 21c4e2de-ec~ 2021-02-02 23:50:00 51458973-404c-58~
## 8 cf3cfc49-d~ tdr:tdr-fp-54~ 50620c50-23~ 2021-02-02 23:50:00 5bbebef4-9b14-50~
## 9 cf3cfc49-d~ tdr:tdr-fp-54~ e3ecdfc2-44~ 2021-02-02 23:55:00 5bc232f2-b77c-52~
## 10 cf3cfc49-d~ tdr:tdr-fp-54~ ae338c4e-65~ 2021-02-02 23:50:00 6326b602-0f63-54~
## 11 cf3cfc49-d~ tdr:tdr-fp-54~ d62c4599-47~ 2020-02-03 01:00:00 7848d80b-6b1d-56~
## 12 cf3cfc49-d~ tdr:tdr-fp-54~ 81df106e-e7~ 2021-02-02 23:55:00 9f8bc032-6276-57~
## 13 cf3cfc49-d~ tdr:tdr-fp-54~ 2838323c-cd~ 2020-02-03 01:00:00 b98cfaac-64f5-59~
## 14 cf3cfc49-d~ tdr:tdr-fp-54~ c3f672ad-e6~ 2021-02-02 23:50:00 bf7751ae-ac9d-5b~
## 15 cf3cfc49-d~ tdr:tdr-fp-54~ a9c90392-ca~ 2020-02-03 01:00:00 c7b6470c-e2f0-51~
## 16 cf3cfc49-d~ tdr:tdr-fp-54~ 9d0f5cd1-0e~ 2020-02-03 01:00:00 d0b95f2c-98ae-58~
## 17 cf3cfc49-d~ tdr:tdr-fp-54~ 59de15e1-f5~ 2021-02-02 23:50:00 d18759a6-2a95-5d~
## 18 cf3cfc49-d~ tdr:tdr-fp-54~ 54fb0e25-57~ 2021-02-02 23:55:00 dfd9905b-d6c9-5a~
## 19 cf3cfc49-d~ tdr:tdr-fp-54~ 7516565a-e8~ 2021-02-02 23:55:00 e07ca731-b20a-5b~
## 20 cf3cfc49-d~ tdr:tdr-fp-54~ 8e850d2d-0b~ 2021-02-02 23:50:00 fd41f3d6-7664-53~
## # ... with 50 more variables: file_type <chr>, file_name <chr>,
## # file_format <chr>, read_index <lgl>, file_size <dbl>, file_uuid <chr>,
## # file_version <dttm>, file_crc32c <chr>, file_sha256 <chr>,
## # file_content_type <chr>, file_drs_uri <chr>, file_url <chr>,
## # cell_suspension.provenance.document_id <chr>,
## # cell_suspension.biomaterial_core.biomaterial_id <chr>,
## # cell_suspension.estimated_cell_count <lgl>, ...file_uuid <- "24a8a323-7ecd-504e-a253-b0e0892dd730"file_hca_tbl for the file based on it’s uuidfile_filter <- hca::filters(
fileId = list(is = file_uuid)
)
file_tbl <- hca::files(filters = file_filter)
file_tbl
## # A tibble: 1 x 8
## fileId name fileFormat size version projectTitle projectId url
## <chr> <chr> <chr> <int> <chr> <chr> <chr> <chr>
## 1 24a8a32~ t-cell~ loom 3.90e8 2021-0~ A single-cell~ 4a95101c-~ https:/~file_location <-
file_tbl |>
hca::files_download()
file_location
## 24a8a323-7ecd-504e-a253-b0e0892dd730-2021-02-11T19:00:05.000000Z
## "C:\\Users\\biocbuild\\AppData\\Local/R/cache/R/hca/1550506589a_1550506589a.loom"LoomExperiment objectloom <- LoomExperiment::import(file_location)
metadata(loom) |>
dplyr::glimpse()
## List of 15
## $ last_modified : chr "20210211T185949.186062Z"
## $ CreationDate : chr "20210211T185658.758915Z"
## $ LOOM_SPEC_VERSION : chr "3.0.0"
## $ donor_organism.genus_species : chr "Homo sapiens"
## $ expression_data_type : chr "exonic"
## $ input_id : chr "58a18a4c-5423-4c59-9b3c-50b7f30b1ca5, c763f679-e13d-4f81-844f-c2c80fc90f46, c76d90b8-c190-4c58-b9bc-b31f586ec7f"| __truncated__
## $ input_id_metadata_field : chr "sequencing_process.provenance.document_id"
## $ input_name : chr "PP012_suspension, PP003_suspension, PP004_suspension, PP011_suspension"
## $ input_name_metadata_field : chr "sequencing_input.biomaterial_core.biomaterial_id"
## $ library_preparation_protocol.library_construction_approach: chr "10X v2 sequencing"
## $ optimus_output_schema_version : chr "1.0.0"
## $ pipeline_version : chr "Optimus_v4.2.2"
## $ project.project_core.project_name : chr "HumanTissueTcellActivation"
## $ project.provenance.document_id : chr "4a95101c-9ffc-4f30-a809-f04518a23803"
## $ specimen_from_organism.organ : chr "hematopoietic system"
colData(loom) |>
dplyr::as_tibble() |>
dplyr::glimpse()
## Rows: 91,713
## Columns: 43
## $ CellID <chr> "GCTTCCATCACCGT~
## $ antisense_reads <int> 0, 0, 0, 0, 0, ~
## $ cell_barcode_fraction_bases_above_30_mean <dbl> 0.9846281, 0.98~
## $ cell_barcode_fraction_bases_above_30_variance <dbl> 0.003249023, 0.~
## $ cell_names <chr> "GCTTCCATCACCGT~
## $ duplicate_reads <int> 0, 0, 0, 0, 0, ~
## $ emptydrops_FDR <dbl> 1.000000000, 0.~
## $ emptydrops_IsCell <raw> 00, 01, 00, 00,~
## $ emptydrops_Limited <raw> 00, 01, 00, 00,~
## $ emptydrops_LogProb <dbl> -689.6831, -120~
## $ emptydrops_PValue <dbl> 0.91840816, 0.0~
## $ emptydrops_Total <int> 255, 16705, 681~
## $ fragments_per_molecule <dbl> 1.693252, 8.453~
## $ fragments_with_single_read_evidence <int> 504, 139828, 58~
## $ genes_detected_multiple_observations <int> 82, 2873, 1552,~
## $ genomic_read_quality_mean <dbl> 36.62988, 36.87~
## $ genomic_read_quality_variance <dbl> 25.99015, 20.19~
## $ genomic_reads_fraction_bases_quality_above_30_mean <dbl> 0.8584288, 0.86~
## $ genomic_reads_fraction_bases_quality_above_30_variance <dbl> 0.03981779, 0.0~
## $ input_id <chr> "58a18a4c-5423-~
## $ molecule_barcode_fraction_bases_above_30_mean <dbl> 0.9820324, 0.98~
## $ molecule_barcode_fraction_bases_above_30_variance <dbl> 0.005782884, 0.~
## $ molecules_with_single_read_evidence <int> 276, 5028, 2041~
## $ n_fragments <int> 552, 202060, 84~
## $ n_genes <int> 227, 3381, 1826~
## $ n_mitochondrial_genes <int> 5, 22, 17, 5, 2~
## $ n_mitochondrial_molecules <int> 8, 3528, 2928, ~
## $ n_molecules <int> 326, 23902, 998~
## $ n_reads <int> 679, 341669, 13~
## $ noise_reads <int> 0, 0, 0, 0, 0, ~
## $ pct_mitochondrial_molecules <dbl> 1.1782032, 1.03~
## $ perfect_cell_barcodes <int> 667, 336674, 13~
## $ perfect_molecule_barcodes <int> 384, 227854, 89~
## $ reads_mapped_exonic <int> 343, 210716, 84~
## $ reads_mapped_intergenic <int> 39, 19439, 8042~
## $ reads_mapped_intronic <int> 175, 58833, 276~
## $ reads_mapped_multiple <int> 162, 90968, 365~
## $ reads_mapped_too_many_loci <int> 0, 0, 0, 0, 0, ~
## $ reads_mapped_uniquely <int> 450, 227309, 93~
## $ reads_mapped_utr <int> 55, 29289, 1039~
## $ reads_per_fragment <dbl> 1.230072, 1.690~
## $ reads_unmapped <int> 67, 23392, 9340~
## $ spliced_reads <int> 99, 73817, 2987~.loom fileThe function optimus_loom_annotation() takes in the file path of a
.loom file generated by the Optimus pipeline and returns a
LoomExperiment object whose colData has been annotated with
additional specimen data extracted from a manifest.
annotated_loom <- optimus_loom_annotation(file_location)
## requesting manifest
annotated_loom
## class: SingleCellLoomExperiment
## dim: 58347 91713
## metadata(16): last_modified CreationDate ...
## specimen_from_organism.organ manifest
## assays(1): matrix
## rownames: NULL
## rowData names(29): Gene antisense_reads ... reads_per_molecule
## spliced_reads
## colnames: NULL
## colData names(97): input_id CellID ...
## sequencing_input.biomaterial_core.biomaterial_id
## sequencing_input_type
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowGraphs(0): NULL
## colGraphs(0): NULL
## new metadata
setdiff(
names(metadata(annotated_loom)),
names(metadata(loom))
)
## [1] "manifest"
metadata(annotated_loom)$manifest
## # A tibble: 4 x 55
## source_id source_spec bundle_uuid bundle_version file_document_id
## <chr> <chr> <chr> <dttm> <chr>
## 1 cf3cfc49-d~ tdr:tdr-fp-546~ e3ecdfc2-44~ 2021-02-02 23:55:00 5bc232f2-b77c-52~
## 2 cf3cfc49-d~ tdr:tdr-fp-546~ 81df106e-e7~ 2021-02-02 23:55:00 9f8bc032-6276-57~
## 3 cf3cfc49-d~ tdr:tdr-fp-546~ 54fb0e25-57~ 2021-02-02 23:55:00 dfd9905b-d6c9-5a~
## 4 cf3cfc49-d~ tdr:tdr-fp-546~ 7516565a-e8~ 2021-02-02 23:55:00 e07ca731-b20a-5b~
## # ... with 50 more variables: file_type <chr>, file_name <chr>,
## # file_format <chr>, read_index <chr>, file_size <dbl>, file_uuid <chr>,
## # file_version <dttm>, file_crc32c <chr>, file_sha256 <chr>,
## # file_content_type <chr>, file_drs_uri <chr>, file_url <chr>,
## # cell_suspension.provenance.document_id <chr>,
## # cell_suspension.biomaterial_core.biomaterial_id <chr>,
## # cell_suspension.estimated_cell_count <lgl>, ...
## new colData columns
setdiff(
names(colData(annotated_loom)),
names(colData(loom))
)
## [1] "source_id"
## [2] "source_spec"
## [3] "bundle_uuid"
## [4] "bundle_version"
## [5] "file_document_id"
## [6] "file_type"
## [7] "file_name"
## [8] "file_format"
## [9] "read_index"
## [10] "file_size"
## [11] "file_uuid"
## [12] "file_version"
## [13] "file_crc32c"
## [14] "file_sha256"
## [15] "file_content_type"
## [16] "file_drs_uri"
## [17] "file_url"
## [18] "cell_suspension.provenance.document_id"
## [19] "cell_suspension.biomaterial_core.biomaterial_id"
## [20] "cell_suspension.estimated_cell_count"
## [21] "cell_suspension.selected_cell_type"
## [22] "sequencing_protocol.instrument_manufacturer_model"
## [23] "sequencing_protocol.paired_end"
## [24] "library_preparation_protocol.library_construction_approach"
## [25] "library_preparation_protocol.nucleic_acid_source"
## [26] "project.provenance.document_id"
## [27] "project.contributors.institution"
## [28] "project.contributors.laboratory"
## [29] "project.project_core.project_short_name"
## [30] "project.project_core.project_title"
## [31] "specimen_from_organism.provenance.document_id"
## [32] "specimen_from_organism.diseases"
## [33] "specimen_from_organism.organ"
## [34] "specimen_from_organism.organ_part"
## [35] "specimen_from_organism.preservation_storage.preservation_method"
## [36] "donor_organism.sex"
## [37] "donor_organism.biomaterial_core.biomaterial_id"
## [38] "donor_organism.provenance.document_id"
## [39] "donor_organism.genus_species"
## [40] "donor_organism.development_stage"
## [41] "donor_organism.diseases"
## [42] "donor_organism.organism_age"
## [43] "cell_line.provenance.document_id"
## [44] "cell_line.biomaterial_core.biomaterial_id"
## [45] "organoid.provenance.document_id"
## [46] "organoid.biomaterial_core.biomaterial_id"
## [47] "organoid.model_organ"
## [48] "organoid.model_organ_part"
## [49] "_entity_type"
## [50] "sample.provenance.document_id"
## [51] "sample.biomaterial_core.biomaterial_id"
## [52] "sequencing_input.provenance.document_id"
## [53] "sequencing_input.biomaterial_core.biomaterial_id"
## [54] "sequencing_input_type"sessionInfo()
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows Server x64 (build 17763)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=C
## [2] LC_CTYPE=English_United States.1252
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.1252
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] hca_1.1.5 LoomExperiment_1.11.1
## [3] BiocIO_1.3.0 rhdf5_2.37.3
## [5] SingleCellExperiment_1.15.2 SummarizedExperiment_1.23.5
## [7] Biobase_2.53.0 GenomicRanges_1.45.0
## [9] GenomeInfoDb_1.29.8 IRanges_2.27.2
## [11] S4Vectors_0.31.5 BiocGenerics_0.39.2
## [13] MatrixGenerics_1.5.4 matrixStats_0.61.0
## [15] dplyr_1.0.7 BiocStyle_2.21.3
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.2 tidyr_1.1.4 sass_0.4.0
## [4] vroom_1.5.5 bit64_4.0.5 jsonlite_1.7.2
## [7] bslib_0.3.0 assertthat_0.2.1 BiocManager_1.30.16
## [10] BiocFileCache_2.1.1 blob_1.2.2 GenomeInfoDbData_1.2.7
## [13] yaml_2.2.1 pillar_1.6.3 RSQLite_2.2.8
## [16] lattice_0.20-45 glue_1.4.2 digest_0.6.28
## [19] XVector_0.33.0 htmltools_0.5.2 Matrix_1.3-4
## [22] pkgconfig_2.0.3 bookdown_0.24 zlibbioc_1.39.0
## [25] purrr_0.3.4 HDF5Array_1.21.0 tzdb_0.1.2
## [28] tibble_3.1.5 generics_0.1.0 ellipsis_0.3.2
## [31] withr_2.4.2 cachem_1.0.6 cli_3.0.1
## [34] magrittr_2.0.1 crayon_1.4.1 memoise_2.0.0
## [37] evaluate_0.14 fansi_0.5.0 tools_4.1.1
## [40] hms_1.1.1 formatR_1.11 lifecycle_1.0.1
## [43] stringr_1.4.0 Rhdf5lib_1.15.2 DelayedArray_0.19.4
## [46] lambda.r_1.2.4 compiler_4.1.1 jquerylib_0.1.4
## [49] rlang_0.4.11 futile.logger_1.4.3 grid_4.1.1
## [52] RCurl_1.98-1.5 rhdf5filters_1.5.0 rappdirs_0.3.3
## [55] bitops_1.0-7 rmarkdown_2.11 DBI_1.1.1
## [58] curl_4.3.2 R6_2.5.1 knitr_1.36
## [61] fastmap_1.1.0 bit_4.0.4 utf8_1.2.2
## [64] filelock_1.0.2 futile.options_1.0.1 readr_2.0.2
## [67] stringi_1.7.5 parallel_4.1.1 Rcpp_1.0.7
## [70] vctrs_0.3.8 dbplyr_2.1.1 tidyselect_1.1.1
## [73] xfun_0.26