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: 70 x 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 7027adc6-c9c… A Cellular Atlas of… <chr [1]> <chr [1]> <chr [1]>
## 3 f86f1ab4-1fb… A Single-Cell Trans… <chr [2]> <chr [1]> <chr [1]>
## 4 c1810dbc-16d… A cell atlas of hum… <chr [2]> <chr [2]> <chr [2]>
## 5 996120f9-e84… A human single cell… <chr [1]> <chr [1]> <chr [1]>
## 6 1defdada-a36… A single-cell molec… <chr [1]> <chr [1]> <chr [1]>
## 7 4a95101c-9ff… A single-cell refer… <chr [1]> <chr [4]> <chr [4]>
## 8 1cd1f41f-f81… A single-cell surve… <chr [1]> <chr [1]> <chr [1]>
## 9 8185730f-411… A single-cell trans… <chr [1]> <chr [1]> <chr [1]>
## 10 38449aea-70b… Altered human oligo… <chr [1]> <chr [1]> <chr [1]>
## # … with 60 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: 25 x 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 7027adc6-c9c… A Cellular Atlas of… <chr [1]> <chr [1]> <chr [1]>
## 2 4a95101c-9ff… A single-cell refer… <chr [1]> <chr [4]> <chr [4]>
## 3 8185730f-411… A single-cell trans… <chr [1]> <chr [1]> <chr [1]>
## 4 38449aea-70b… Altered human oligo… <chr [1]> <chr [1]> <chr [1]>
## 5 ad98d3cd-26f… Cells of the adult … <chr [1]> <chr [1]> <chr [1]>
## 6 cc95ff89-2e6… Census of Immune Ce… <chr [1]> <chr [2]> <chr [2]>
## 7 f2fe82f0-445… Decoding the develo… <chr [1]> <chr [4]> <chr [4]>
## 8 b4a7d12f-6c2… Defining the Activa… <chr [1]> <chr [1]> <chr [1]>
## 9 4d6f6c96-2a8… Dissecting the huma… <chr [1]> <chr [1]> <chr [1]>
## 10 83f5188e-3bf… Distinct microbial … <chr [1]> <chr [2]> <chr [2]>
## # … with 15 more rowsUse standard R commands to further filter projects to the one we are
interested in, with title starting with “Single cell
trans…”. Extract the unique projectId for this project.
project_tibble %>%
filter(startsWith(projectTitle, "Single")) %>%
t()
## [,1]
## 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"
## [,2]
## projectId "2ef3655a-973d-4d69-9b41-21fa4041eed7"
## projectTitle "Single-cell RNA sequencing of normal human kidney"
## genusSpecies "Homo sapiens"
## samples.organ "kidney"
## specimens.organ "kidney"
## [,3]
## 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"
## [,4]
## 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"
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 x 7
## fileId name fileFormat size version projectTitle url
## <chr> <chr> <chr> <int> <chr> <chr> <chr>
## 1 267d8c8f… reprogra… loom 1.16e8 2021-02-… Single cell prof… https://se…
## 2 ed5e6907… 7801fd50… loom 9.42e8 2021-02-… Single cell prof… https://se…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 18025
## metadata(0):
## 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: 34 x 3
## facet n_terms n_values
## <chr> <int> <int>
## 1 assayType 1 70
## 2 biologicalSex 4 117
## 3 cellLineType 5 73
## 4 contactName 791 910
## 5 developmentStage 44 126
## 6 donorDisease 100 175
## 7 effectiveOrgan 48 120
## 8 fileFormat 25 220
## 9 fileSource 9 165
## 10 genusSpecies 3 79
## # … with 24 more rowsNote the fileFormat facet, and repeat projects_facets() to
discover detail about available file formats
projects_facets("fileFormat")
## # A tibble: 25 x 3
## facet term count
## <chr> <chr> <int>
## 1 fileFormat fastq.gz 68
## 2 fileFormat bam 25
## 3 fileFormat loom 25
## 4 fileFormat csv 16
## 5 fileFormat tar 16
## 6 fileFormat h5ad 9
## 7 fileFormat zip 9
## 8 fileFormat pdf 8
## 9 fileFormat txt.gz 8
## 10 fileFormat mtx.gz 4
## # … 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: 9 x 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 c1810dbc-16d… A cell atlas of huma… <chr [2]> <chr [2]> <chr [2]>
## 2 ad98d3cd-26f… Cells of the adult h… <chr [1]> <chr [1]> <chr [1]>
## 3 83f5188e-3bf… Distinct microbial a… <chr [1]> <chr [2]> <chr [2]>
## 4 c4077b3c-5c9… Ischaemic sensitivit… <chr [1]> <chr [3]> <chr [3]>
## 5 091cf39b-01b… Profiling of CD34+ c… <chr [1]> <chr [0]> <chr [1]>
## 6 f83165c5-e2e… Reconstructing the h… <chr [1]> <chr [3]> <chr [3]>
## 7 abe1a013-af7… Spatio-temporal immu… <chr [1]> <chr [1]> <chr [1]>
## 8 4e6f083b-5b9… The emergent landsca… <chr [1]> <chr [3]> <chr [3]>
## 9 455b46e6-d8e… Transcriptomic chara… <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
## 70 8 35hits 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]]$projects[[1]])
## projectTitle projectShortname laboratory
## 1 1 1
## projectDescription contributors publications
## 1 6 1
## arrayExpressAccessions geoSeriesAccessions insdcProjectAccessions
## 1 1 1
## insdcStudyAccessions supplementaryLinks matrices
## 1 1 0
## contributorMatrices
## 1
projects_list$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: 2146
## # total number of elements: 25873
## # number of leaf paths: 1380
## # number of leaf elements: 18177
## # lol_path():
## # A tibble: 2,146 x 3
## path n is_leaf
## <chr> <int> <lgl>
## 1 hits 1 FALSE
## 2 hits[*] 70 FALSE
## 3 hits[*].cellLines 70 FALSE
## 4 hits[*].cellLines[*] 6 FALSE
## 5 hits[*].cellLines[*].cellLineType 6 FALSE
## 6 hits[*].cellLines[*].cellLineType[*] 9 TRUE
## 7 hits[*].cellLines[*].id 6 FALSE
## 8 hits[*].cellLines[*].id[*] 27 TRUE
## 9 hits[*].cellLines[*].modelOrgan 6 FALSE
## 10 hits[*].cellLines[*].modelOrgan[*] 9 TRUE
## # … with 2,136 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: 2035
## # total number of elements: 12808
## # number of leaf paths: 1331
## # number of leaf elements: 9688
## # lol_path():
## # A tibble: 2,035 x 3
## path n is_leaf
## <chr> <int> <lgl>
## 1 hits[*].projects[*] 70 FALSE
## 2 hits[*].projects[*].arrayExpressAccessions 70 FALSE
## 3 hits[*].projects[*].arrayExpressAccessions[*] 76 TRUE
## 4 hits[*].projects[*].contributorMatrices 70 FALSE
## 5 hits[*].projects[*].contributorMatrices.developmentStage 2 FALSE
## 6 hits[*].projects[*].contributorMatrices.developmentStage.adult 2 FALSE
## 7 hits[*].projects[*].contributorMatrices.developmentStage.adult… 1 FALSE
## 8 hits[*].projects[*].contributorMatrices.developmentStage.adult… 1 FALSE
## 9 hits[*].projects[*].contributorMatrices.developmentStage.adult… 1 FALSE
## 10 hits[*].projects[*].contributorMatrices.developmentStage.adult… 1 FALSE
## # … with 2,025 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 x 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] 70
head(titles, 2)
## [1] "1.3 Million Brain Cells from E18 Mice"
## [2] "A Cellular Atlas of Pitx2-Dependent Cardiac Development."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",
organ = "hits[*].cellSuspensions[*].organ[*]",
totalCells = "hits[*].cellSuspensions[*].totalCells"
)
projects <- projects(filters, columns = columns)
projects
## # A tibble: 9 x 6
## projectId projectTitle genusSpecies donorCount organ totalCells
## <chr> <chr> <list> <int> <lis> <list>
## 1 c1810dbc-16d2… A cell atlas of human… <chr [2]> 24 <chr… <int [2]>
## 2 ad98d3cd-26fb… Cells of the adult hu… <chr [1]> 14 <chr… <int [1]>
## 3 83f5188e-3bf7… Distinct microbial an… <chr [1]> 6 <chr… <int [2]>
## 4 c4077b3c-5c98… Ischaemic sensitivity… <chr [1]> 14 <chr… <int [3]>
## 5 091cf39b-01bc… Profiling of CD34+ ce… <chr [1]> 3 <chr… <int [1]>
## 6 f83165c5-e2ea… Reconstructing the hu… <chr [1]> 16 <chr… <int [0]>
## 7 abe1a013-af7a… Spatio-temporal immun… <chr [1]> 8 <chr… <int [0]>
## 8 4e6f083b-5b9a… The emergent landscap… <chr [1]> 6 <chr… <int [3]>
## 9 455b46e6-d8ea… Transcriptomic charac… <chr [1]> 4 <chr… <int [3]>Note that the organ and totalCells columns have more than one
entry per project.
projects |>
select(projectId, organ, totalCells)
## # A tibble: 9 x 3
## projectId 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 4e6f083b-5b9a-4393-9890-2a83da8188f1 <chr [3]> <int [3]>
## 9 455b46e6-d8ea-4611-861e-de720a562ada <chr [3]> <int [3]>In this case, the mapping between organ and totalCells is clear,
but in general more refined navigation of the lol structure may be
necessary.
projects |>
select(projectId, organ, totalCells) |>
filter(lengths(totalCells) > 0) |>
tidyr::unnest(c("organ", "totalCells"))
## # A tibble: 15 x 3
## projectId 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 large intestine 1141
## 5 83f5188e-3bf7-4956-9544-cea4f8997756 immune organ 381
## 6 c4077b3c-5c98-4d26-a614-246d12c2e5d7 esophagus 93267
## 7 c4077b3c-5c98-4d26-a614-246d12c2e5d7 lung 40025
## 8 c4077b3c-5c98-4d26-a614-246d12c2e5d7 spleen 66553
## 9 091cf39b-01bc-42e5-9437-f419a66c8a45 hematopoietic system 1480000
## 10 4e6f083b-5b9a-4393-9890-2a83da8188f1 presumptive gut 30952
## 11 4e6f083b-5b9a-4393-9890-2a83da8188f1 embryo 27083
## 12 4e6f083b-5b9a-4393-9890-2a83da8188f1 endoderm 54166
## 13 455b46e6-d8ea-4611-861e-de720a562ada spleen 60043
## 14 455b46e6-d8ea-4611-861e-de720a562ada bone marrow 87532
## 15 455b46e6-d8ea-4611-861e-de720a562ada blood 25016Select the following entry, augment the filter, and query available files
projects %>%
filter(startsWith(projectTitle, "Reconstruct")) %>%
t()
## [,1]
## projectId "f83165c5-e2ea-4d15-a5cf-33f3550bffde"
## projectTitle "Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics"
## genusSpecies "Homo sapiens"
## donorCount 16
## 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"
## url "https://service.azul.data.humancellatlas.org/repository/files/6d4fedcf-857d-5fbb-9928-8b9605500a69?version=2021-02-10T16%3A56%3A40.419579Z&catalog=dcp4"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 x 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 x 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 7027adc6-c9c… A Cellular Atlas of… <chr [1]> <chr [1]> <chr [1]>
## 3 f86f1ab4-1fb… A Single-Cell Trans… <chr [2]> <chr [1]> <chr [1]>
## 4 c1810dbc-16d… A cell atlas of hum… <chr [2]> <chr [2]> <chr [2]>
## 5 996120f9-e84… A human single cell… <chr [1]> <chr [1]> <chr [1]>
## 6 1defdada-a36… A single-cell molec… <chr [1]> <chr [1]> <chr [1]>
## 7 4a95101c-9ff… A single-cell refer… <chr [1]> <chr [4]> <chr [4]>
## 8 1cd1f41f-f81… A single-cell surve… <chr [1]> <chr [1]> <chr [1]>
## 9 8185730f-411… A single-cell trans… <chr [1]> <chr [1]> <chr [1]>
## 10 38449aea-70b… Altered human oligo… <chr [1]> <chr [1]> <chr [1]>
## # … with 20 more rows
page_2_tbl <- page_1_tbl %>% hca_next()
page_2_tbl
## # A tibble: 30 x 5
## projectId projectTitle genusSpecies samples.organ specimens.organ
## <chr> <chr> <list> <list> <list>
## 1 5b5f05b7-248… Integrative computa… <chr [1]> <chr [1]> <chr [1]>
## 2 c4077b3c-5c9… Ischaemic sensitivi… <chr [1]> <chr [3]> <chr [3]>
## 3 1c6a960d-52a… Massively parallel … <chr [1]> <chr [1]> <chr [1]>
## 4 8c3c290d-dff… Melanoma infiltrati… <chr [1]> <chr [3]> <chr [3]>
## 5 90bd6933-40c… Precursors of human… <chr [1]> <chr [1]> <chr [1]>
## 6 091cf39b-01b… Profiling of CD34+ … <chr [1]> <chr [0]> <chr [1]>
## 7 7adede6a-0ab… RNA Sequencing of S… <chr [1]> <chr [1]> <chr [1]>
## 8 f83165c5-e2e… Reconstructing the … <chr [1]> <chr [3]> <chr [3]>
## 9 c41dffbf-ad8… Resolving the fibro… <chr [2]> <chr [2]> <chr [2]>
## 10 ce33dde2-382… Single Cell RNA-Seq… <chr [1]> <chr [1]> <chr [1]>
## # … with 20 more rows
## should be identical to page_1_tbl
page_2_tbl %>% hca_prev()
## # A tibble: 30 x 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 7027adc6-c9c… A Cellular Atlas of… <chr [1]> <chr [1]> <chr [1]>
## 3 f86f1ab4-1fb… A Single-Cell Trans… <chr [2]> <chr [1]> <chr [1]>
## 4 c1810dbc-16d… A cell atlas of hum… <chr [2]> <chr [2]> <chr [2]>
## 5 996120f9-e84… A human single cell… <chr [1]> <chr [1]> <chr [1]>
## 6 1defdada-a36… A single-cell molec… <chr [1]> <chr [1]> <chr [1]>
## 7 4a95101c-9ff… A single-cell refer… <chr [1]> <chr [4]> <chr [4]>
## 8 1cd1f41f-f81… A single-cell surve… <chr [1]> <chr [1]> <chr [1]>
## 9 8185730f-411… A single-cell trans… <chr [1]> <chr [1]> <chr [1]>
## 10 38449aea-70b… Altered human oligo… <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 Atlas of Pitx2-Dependent Cardiac Development."
## [3] "A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure"
## [4] "A cell atlas of human thymic development defines T cell repertoire formation"
## [5] "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."
page_2_lol <-
page_1_lol %>%
hca_next()
page_2_lol %>%
lol_pull("hits[*].projects[*].projectTitle")
## [1] "A single-cell molecular map of mouse gastrulation and early organogenesis"
## [2] "A single-cell reference map of transcriptional states for human blood and tissue T cell activation"
## [3] "A single-cell survey of the human first-trimester placenta and decidua"
## [4] "A single-cell transcriptome atlas of the adult human retina"
## [5] "Altered human oligodendrocyte heterogeneity in multiple sclerosis"
## 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 Atlas of Pitx2-Dependent Cardiac Development."
## [3] "A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure"
## [4] "A cell atlas of human thymic development defines T cell repertoire formation"
## [5] "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."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 x 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 x 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: 3 x 3
## fileType count totalSize
## <chr> <int> <dbl>
## 1 fastq.gz 27844 4054335744217
## 2 loom 168 323739761632
## 3 bam 164 3284598129743
first_catalog <- catalogs()[1]
summary(type = "overview", catalog = first_catalog)
## # A tibble: 8 x 2
## name value
## <chr> <dbl>
## 1 totalFileSize 6.67e13
## 2 fileCount 3.03e 5
## 3 donorCount 6.98e 2
## 4 specimenCount 3.00e 3
## 5 speciesCount 3 e 0
## 6 projectCount 7 e 1
## 7 labCount 2.1 e 2
## 8 totalCellCount 7.24e 6Each 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 x 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 e0009214-c0a… Tabula Muris: Transc… Mus musculus <chr [18]> <chr [18]>
## 4 2086eb05-10b… Transcriptomic Profi… Mus musculus <chr [1]> <chr [1]>
projectId <-
heart_projects %>%
filter(
startsWith(
projectTitle,
"Cells of the adult human"
)
) %>%
dplyr::pull(projectId)
projects_detail(uuid = projectId)
## $protocols
## $protocols[[1]]
## $protocols[[1]]$workflow
## $protocols[[1]]$workflow[[1]]
## [1] "optimus_post_processing_v1.0.0"
##
## $protocols[[1]]$workflow[[2]]
## [1] "optimus_v4.2.2"
##
##
##
## $protocols[[2]]
## $protocols[[2]]$libraryConstructionApproach
## $protocols[[2]]$libraryConstructionApproach[[1]]
## [1] "10X 3' v2 sequencing"
##
## $protocols[[2]]$libraryConstructionApproach[[2]]
## [1] "10x 3' v3 sequencing"
##
##
## $protocols[[2]]$nucleicAcidSource
## $protocols[[2]]$nucleicAcidSource[[1]]
## [1] "single cell"
##
## $protocols[[2]]$nucleicAcidSource[[2]]
## [1] "single nucleus"
##
##
##
## $protocols[[3]]
## $protocols[[3]]$instrumentManufacturerModel
## $protocols[[3]]$instrumentManufacturerModel[[1]]
## [1] "Illumina HiSeq 4000"
##
## $protocols[[3]]$instrumentManufacturerModel[[2]]
## [1] "Illumina NextSeq 500"
##
##
## $protocols[[3]]$pairedEnd
## $protocols[[3]]$pairedEnd[[1]]
## [1] FALSE
##
##
##
##
## $entryId
## [1] "ad98d3cd-26fb-4ee3-99c9-8a2ab085e737"
##
## $sources
## $sources[[1]]
## $sources[[1]]$sourceId
## [1] "a56f2a96-cd95-4369-a575-98dcc63be9b6"
##
## $sources[[1]]$sourceName
## [1] "tdr:broad-datarepo-terra-prod-hca2:snapshot/hca_prod_20201120_dcp2___20210401_dcp4:"
##
##
##
## $projects
## $projects[[1]]
## $projects[[1]]$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] "HMGU"
##
## $projects[[1]]$contributors[[1]]$contactName
## [1] "Matthias,,Heinig"
##
## $projects[[1]]$contributors[[1]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[1]]$laboratory
## [1] "Institute of Computational Biology (ICB)"
##
## $projects[[1]]$contributors[[1]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[1]]$email
## [1] "matthias.heinig@helmholtz-muenchen.de"
##
##
## $projects[[1]]$contributors[[2]]
## $projects[[1]]$contributors[[2]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[2]]$contactName
## [1] "Norbert,,Hübner"
##
## $projects[[1]]$contributors[[2]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[2]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[2]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[2]]$email
## [1] "nhuebner@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[3]]
## $projects[[1]]$contributors[[3]]$institution
## [1] "Cambridge Biorepository for Translational Medicine"
##
## $projects[[1]]$contributors[[3]]$contactName
## [1] "Kourosh,,Saeb-Parsy"
##
## $projects[[1]]$contributors[[3]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[3]]$laboratory
## NULL
##
## $projects[[1]]$contributors[[3]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[3]]$email
## [1] "ks10014@cam.ac.uk"
##
##
## $projects[[1]]$contributors[[4]]
## $projects[[1]]$contributors[[4]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[4]]$contactName
## [1] "Liz,,Tuck"
##
## $projects[[1]]$contributors[[4]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[4]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[4]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[4]]$email
## [1] "et2@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[5]]
## $projects[[1]]$contributors[[5]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[5]]$contactName
## [1] "Emily,,Nadelmann"
##
## $projects[[1]]$contributors[[5]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[5]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[5]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[5]]$email
## [1] "Emily_Nadelmann@hms.harvard.edu"
##
##
## $projects[[1]]$contributors[[6]]
## $projects[[1]]$contributors[[6]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[6]]$contactName
## [1] "Catherine,L.,Worth"
##
## $projects[[1]]$contributors[[6]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[6]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[6]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[6]]$email
## [1] "catherine.sargent@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[7]]
## $projects[[1]]$contributors[[7]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[7]]$contactName
## [1] "Sarah,A.,Teichmann"
##
## $projects[[1]]$contributors[[7]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[7]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[7]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[7]]$email
## [1] "st9@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[8]]
## $projects[[1]]$contributors[[8]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[8]]$contactName
## [1] "Joseph,J.,Boyle"
##
## $projects[[1]]$contributors[[8]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[8]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[8]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[8]]$email
## [1] "joseph.boyle@imperial.ac.uk"
##
##
## $projects[[1]]$contributors[[9]]
## $projects[[1]]$contributors[[9]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[9]]$contactName
## [1] "Joshua,M,Gorham"
##
## $projects[[1]]$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] "jgorham@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[10]]
## $projects[[1]]$contributors[[10]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[10]]$contactName
## [1] "Sara,,Samari"
##
## $projects[[1]]$contributors[[10]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[10]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[10]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[10]]$email
## [1] "sara.samari13@imperial.ac.uk"
##
##
## $projects[[1]]$contributors[[11]]
## $projects[[1]]$contributors[[11]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[11]]$contactName
## [1] "Christine,,Seidman"
##
## $projects[[1]]$contributors[[11]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[11]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[11]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[11]]$email
## [1] "cseidman@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[12]]
## $projects[[1]]$contributors[[12]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[12]]$contactName
## [1] "Krzysztof,,Polanski"
##
## $projects[[1]]$contributors[[12]]$projectRole
## [1] "computational scientist"
##
## $projects[[1]]$contributors[[12]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[12]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[12]]$email
## [1] "kp9@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[13]]
## $projects[[1]]$contributors[[13]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[13]]$contactName
## [1] "Daniel,,Reichart"
##
## $projects[[1]]$contributors[[13]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[13]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[13]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[13]]$email
## [1] "Daniel_Reichart@hms.harvard.edu"
##
##
## $projects[[1]]$contributors[[14]]
## $projects[[1]]$contributors[[14]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[14]]$contactName
## [1] "Giannino,,Patone"
##
## $projects[[1]]$contributors[[14]]$projectRole
## [1] "computational scientist"
##
## $projects[[1]]$contributors[[14]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[14]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[14]]$email
## [1] "Giannino.Patone@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[15]]
## $projects[[1]]$contributors[[15]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[15]]$contactName
## [1] "Carlos,,Talavera-López"
##
## $projects[[1]]$contributors[[15]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[15]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[15]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[15]]$email
## [1] "ct5@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[16]]
## $projects[[1]]$contributors[[16]]$institution
## [1] "Sun-Yat Sen University"
##
## $projects[[1]]$contributors[[16]]$contactName
## [1] "Hongbo,,Zhang"
##
## $projects[[1]]$contributors[[16]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[16]]$laboratory
## [1] "Department of Histology and Embryology of Zhongshan School of Medicine"
##
## $projects[[1]]$contributors[[16]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[16]]$email
## [1] "hz3@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[17]]
## $projects[[1]]$contributors[[17]]$institution
## [1] "University of Alberta"
##
## $projects[[1]]$contributors[[17]]$contactName
## [1] "Hao,,Zhang"
##
## $projects[[1]]$contributors[[17]]$projectRole
## [1] "biomaterial provider"
##
## $projects[[1]]$contributors[[17]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
##
## $projects[[1]]$contributors[[17]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[17]]$email
## [1] "hzhang10@ualberta.ca"
##
##
## $projects[[1]]$contributors[[18]]
## $projects[[1]]$contributors[[18]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[18]]$contactName
## [1] "J.,G.,Seidman"
##
## $projects[[1]]$contributors[[18]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[18]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[18]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[18]]$email
## [1] "seidman@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[19]]
## $projects[[1]]$contributors[[19]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[19]]$contactName
## [1] "Henrike,,Maatz"
##
## $projects[[1]]$contributors[[19]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[19]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[19]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[19]]$email
## [1] "h.maatz@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[20]]
## $projects[[1]]$contributors[[20]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[20]]$contactName
## [1] "Hiroko,,Wakimoto"
##
## $projects[[1]]$contributors[[20]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[20]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[20]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[20]]$email
## [1] "hwakimoto@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[21]]
## $projects[[1]]$contributors[[21]]$institution
## [1] "Brigham and Women’s Hospital"
##
## $projects[[1]]$contributors[[21]]$contactName
## [1] "Barbara,,McDonough"
##
## $projects[[1]]$contributors[[21]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[21]]$laboratory
## [1] "Cardiovascular Division"
##
## $projects[[1]]$contributors[[21]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[21]]$email
## [1] "mcdonough@genetics.med.harvard.edu"
##
##
## $projects[[1]]$contributors[[22]]
## $projects[[1]]$contributors[[22]]$institution
## [1] "University of Alberta"
##
## $projects[[1]]$contributors[[22]]$contactName
## [1] "Gavin,,Oudit"
##
## $projects[[1]]$contributors[[22]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[22]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
##
## $projects[[1]]$contributors[[22]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[22]]$email
## [1] "gavin.oudit@ualberta.ca"
##
##
## $projects[[1]]$contributors[[23]]
## $projects[[1]]$contributors[[23]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[23]]$contactName
## [1] "Masatoshi,,Kanda"
##
## $projects[[1]]$contributors[[23]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[23]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[23]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[23]]$email
## [1] "masatoshi.kanda@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[24]]
## $projects[[1]]$contributors[[24]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[24]]$contactName
## [1] "Omer,,Bayraktar"
##
## $projects[[1]]$contributors[[24]]$projectRole
## [1] "co-investigator"
##
## $projects[[1]]$contributors[[24]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[24]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[24]]$email
## [1] "ob5@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[25]]
## $projects[[1]]$contributors[[25]]$institution
## [1] "EMBL-EBI"
##
## $projects[[1]]$contributors[[25]]$contactName
## [1] "Marion,F,Shadbolt"
##
## $projects[[1]]$contributors[[25]]$projectRole
## [1] "data curator"
##
## $projects[[1]]$contributors[[25]]$laboratory
## [1] "Human Cell Atlas Data Coordination Platform"
##
## $projects[[1]]$contributors[[25]]$correspondingContributor
## [1] FALSE
##
## $projects[[1]]$contributors[[25]]$email
## [1] "mshadbolt@ebi.ac.uk"
##
##
## $projects[[1]]$contributors[[26]]
## $projects[[1]]$contributors[[26]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[26]]$contactName
## [1] "Monika,,Litviňuková"
##
## $projects[[1]]$contributors[[26]]$projectRole
## [1] "lead analyst"
##
## $projects[[1]]$contributors[[26]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[26]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[26]]$email
## [1] "monika.litvinukova@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[27]]
## $projects[[1]]$contributors[[27]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
##
## $projects[[1]]$contributors[[27]]$contactName
## [1] "Eric,L.,Lindberg"
##
## $projects[[1]]$contributors[[27]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[27]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
##
## $projects[[1]]$contributors[[27]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[27]]$email
## [1] "Eric.Lindberg@mdc-berlin.de"
##
##
## $projects[[1]]$contributors[[28]]
## $projects[[1]]$contributors[[28]]$institution
## [1] "University of Alberta"
##
## $projects[[1]]$contributors[[28]]$contactName
## [1] "Anissa,,Viveiros"
##
## $projects[[1]]$contributors[[28]]$projectRole
## [1] "biomaterial provider"
##
## $projects[[1]]$contributors[[28]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
##
## $projects[[1]]$contributors[[28]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[28]]$email
## [1] "aviveiro@ualberta.ca"
##
##
## $projects[[1]]$contributors[[29]]
## $projects[[1]]$contributors[[29]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[29]]$contactName
## [1] "Kenny,,Roberts"
##
## $projects[[1]]$contributors[[29]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[29]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[29]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[29]]$email
## [1] "kr19@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[30]]
## $projects[[1]]$contributors[[30]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[30]]$contactName
## [1] "Michela,,Noseda"
##
## $projects[[1]]$contributors[[30]]$projectRole
## [1] "principal investigator"
##
## $projects[[1]]$contributors[[30]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[30]]$correspondingContributor
## [1] TRUE
##
## $projects[[1]]$contributors[[30]]$email
## [1] "m.noseda@imperial.ac.uk"
##
##
## $projects[[1]]$contributors[[31]]
## $projects[[1]]$contributors[[31]]$institution
## [1] "Wellcome Sanger Institute"
##
## $projects[[1]]$contributors[[31]]$contactName
## [1] "Eirini,S.,Fasouli"
##
## $projects[[1]]$contributors[[31]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[31]]$laboratory
## [1] "Cellular Genetics"
##
## $projects[[1]]$contributors[[31]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[31]]$email
## [1] "ef5@sanger.ac.uk"
##
##
## $projects[[1]]$contributors[[32]]
## $projects[[1]]$contributors[[32]]$institution
## [1] "Cambridge Biorepository for Translational Medicine"
##
## $projects[[1]]$contributors[[32]]$contactName
## [1] "Krishnaa,T.,Mahbubani"
##
## $projects[[1]]$contributors[[32]]$projectRole
## [1] "biomaterial provider"
##
## $projects[[1]]$contributors[[32]]$laboratory
## NULL
##
## $projects[[1]]$contributors[[32]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[32]]$email
## [1] "ktam2@cam.ac.uk"
##
##
## $projects[[1]]$contributors[[33]]
## $projects[[1]]$contributors[[33]]$institution
## [1] "Imperial College London"
##
## $projects[[1]]$contributors[[33]]$contactName
## [1] "Michael,,Lee"
##
## $projects[[1]]$contributors[[33]]$projectRole
## [1] "analyst"
##
## $projects[[1]]$contributors[[33]]$laboratory
## [1] "National Heart and Lung Institute"
##
## $projects[[1]]$contributors[[33]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[33]]$email
## [1] "michael.lee@imperial.ac.uk"
##
##
## $projects[[1]]$contributors[[34]]
## $projects[[1]]$contributors[[34]]$institution
## [1] "Harvard Medical School"
##
## $projects[[1]]$contributors[[34]]$contactName
## [1] "Daniel,,DeLaughter"
##
## $projects[[1]]$contributors[[34]]$projectRole
## [1] "experimental scientist"
##
## $projects[[1]]$contributors[[34]]$laboratory
## [1] "Department of Genetics"
##
## $projects[[1]]$contributors[[34]]$correspondingContributor
## NULL
##
## $projects[[1]]$contributors[[34]]$email
## [1] "Daniel_DeLaughter@hms.harvard.edu"
##
##
##
## $projects[[1]]$publications
## $projects[[1]]$publications[[1]]
## $projects[[1]]$publications[[1]]$publicationTitle
## [1] "Cells of the adult human heart"
##
## $projects[[1]]$publications[[1]]$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]]$size
## [1] 3255905369
##
## $projects[[1]]$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]]$source
## [1] "DCP/2 Analysis"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$uuid
## [1] "b0cd671e-a918-51db-ba29-e127caf325c5"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$version
## [1] "2021-02-13T01:32:57.000000Z"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b0cd671e-a918-51db-ba29-e127caf325c5?version=2021-02-13T01%3A32%3A57.000000Z&catalog=dcp4"
##
##
##
## $projects[[1]]$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]]$size
## [1] 4398007571
##
## $projects[[1]]$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]]$source
## [1] "DCP/2 Analysis"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "dc58c876-3de2-5264-b108-531d4e6c914a"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-15T14:15:05.000000Z"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/dc58c876-3de2-5264-b108-531d4e6c914a?version=2021-02-15T14%3A15%3A05.000000Z&catalog=dcp4"
##
##
##
##
##
## $projects[[1]]$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]]$size
## [1] 4398007571
##
## $projects[[1]]$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]]$source
## [1] "DCP/2 Analysis"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "dc58c876-3de2-5264-b108-531d4e6c914a"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-15T14:15:05.000000Z"
##
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/dc58c876-3de2-5264-b108-531d4e6c914a?version=2021-02-15T14%3A15%3A05.000000Z&catalog=dcp4"
##
##
##
##
##
##
##
##
##
##
##
## $projects[[1]]$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]]$size
## [1] 5068859764
##
## $projects[[1]]$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]]$source
## [1] "Contributor"
##
## $projects[[1]]$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]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b30d1a16-fb04-5ac7-999f-6ce9d1de0c76?version=2021-02-10T17%3A01%3A03.177554Z&catalog=dcp4"
##
##
##
## $projects[[1]]$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]]$size
## [1] 5068859764
##
## $projects[[1]]$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]]$source
## [1] "Contributor"
##
## $projects[[1]]$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]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b30d1a16-fb04-5ac7-999f-6ce9d1de0c76?version=2021-02-10T17%3A01%3A03.177554Z&catalog=dcp4"
##
##
##
##
##
##
##
##
##
##
##
##
##
## $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]]
## $fileTypeSummaries[[1]]$fileType
## [1] "fastq.gz"
##
## $fileTypeSummaries[[1]]$count
## [1] 768
##
## $fileTypeSummaries[[1]]$totalSize
## [1] 3.05423e+12
##
## $fileTypeSummaries[[1]]$source
## $fileTypeSummaries[[1]]$source[[1]]
## NULL
##
##
##
## $fileTypeSummaries[[2]]
## $fileTypeSummaries[[2]]$fileType
## [1] "loom"
##
## $fileTypeSummaries[[2]]$count
## [1] 150
##
## $fileTypeSummaries[[2]]$totalSize
## [1] 294514137285
##
## $fileTypeSummaries[[2]]$source
## $fileTypeSummaries[[2]]$source[[1]]
## [1] "DCP/2 Analysis"
##
## $fileTypeSummaries[[2]]$source[[2]]
## NULL
##
##
##
## $fileTypeSummaries[[3]]
## $fileTypeSummaries[[3]]$fileType
## [1] "bam"
##
## $fileTypeSummaries[[3]]$count
## [1] 148
##
## $fileTypeSummaries[[3]]$totalSize
## [1] 2.703466e+12
##
## $fileTypeSummaries[[3]]$source
## $fileTypeSummaries[[3]]$source[[1]]
## NULL
##
##
##
## $fileTypeSummaries[[4]]
## $fileTypeSummaries[[4]]$fileType
## [1] "h5ad"
##
## $fileTypeSummaries[[4]]$count
## [1] 1
##
## $fileTypeSummaries[[4]]$totalSize
## [1] 5068859764
##
## $fileTypeSummaries[[4]]$source
## $fileTypeSummaries[[4]]$source[[1]]
## [1] "Contributor"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_1.0.0 LoomExperiment_1.10.0
## [3] BiocIO_1.2.0 rhdf5_2.36.0
## [5] SingleCellExperiment_1.14.0 SummarizedExperiment_1.22.0
## [7] Biobase_2.52.0 GenomicRanges_1.44.0
## [9] GenomeInfoDb_1.28.0 IRanges_2.26.0
## [11] MatrixGenerics_1.4.0 matrixStats_0.58.0
## [13] S4Vectors_0.30.0 BiocGenerics_0.38.0
## [15] dplyr_1.0.6 httr_1.4.2
## [17] BiocStyle_2.20.0
##
## 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_1.30.15 BiocFileCache_2.0.0 blob_1.2.1
## [10] GenomeInfoDbData_1.2.6 yaml_2.2.1 pillar_1.6.1
## [13] RSQLite_2.2.7 lattice_0.20-44 glue_1.4.2
## [16] digest_0.6.27 XVector_0.32.0 htmltools_0.5.1.1
## [19] Matrix_1.3-3 pkgconfig_2.0.3 bookdown_0.22
## [22] zlibbioc_1.38.0 purrr_0.3.4 HDF5Array_1.20.0
## [25] tibble_3.1.2 generics_0.1.0 ellipsis_0.3.2
## [28] withr_2.4.2 cachem_1.0.5 cli_2.5.0
## [31] magrittr_2.0.1 crayon_1.4.1 ps_1.6.0
## [34] memoise_2.0.0 evaluate_0.14 fansi_0.4.2
## [37] tools_4.1.0 lifecycle_1.0.0 stringr_1.4.0
## [40] Rhdf5lib_1.14.0 DelayedArray_0.18.0 compiler_4.1.0
## [43] jquerylib_0.1.4 rlang_0.4.11 grid_4.1.0
## [46] RCurl_1.98-1.3 rstudioapi_0.13 rhdf5filters_1.4.0
## [49] rappdirs_0.3.3 bitops_1.0-7 rmarkdown_2.8
## [52] DBI_1.1.1 curl_4.3.1 R6_2.5.0
## [55] knitr_1.33 fastmap_1.1.0 bit_4.0.4
## [58] utf8_1.2.1 filelock_1.0.2 stringi_1.6.2
## [61] Rcpp_1.0.6 vctrs_0.3.8 dbplyr_2.1.1
## [64] tidyselect_1.1.1 xfun_0.23