Contents

1 Motivation & Introduction

The 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.

1.1 Installation and getting started

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)

2 Example: Discover and download a ‘loom’ file

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.

2.1 Discover projects with loom files

Use projects() to retrieve all projects in the HCA’s default catalog.

projects()
## # A tibble: 165 × 5
##    projectId     projectTitle         genusSpecies samples.organ specimens.organ
##    <chr>         <chr>                <list>       <list>        <list>         
##  1 74b6d569-3b1… 1.3 Million Brain C… <chr [1]>    <chr [1]>     <chr [1]>      
##  2 53c53cd4-812… A Cellular Anatomy … <chr [1]>    <chr [1]>     <chr [1]>      
##  3 7027adc6-c9c… A Cellular Atlas of… <chr [1]>    <chr [1]>     <chr [1]>      
##  4 60ea42e1-af4… A Protocol for Reve… <chr [1]>    <chr [1]>     <chr [1]>      
##  5 f86f1ab4-1fb… A Single-Cell Trans… <chr [2]>    <chr [1]>     <chr [1]>      
##  6 602628d7-c03… A Single-cell Trans… <chr [1]>    <chr [3]>     <chr [3]>      
##  7 c1810dbc-16d… A cell atlas of hum… <chr [2]>    <chr [2]>     <chr [2]>      
##  8 a9301beb-e9f… A human cell atlas … <chr [1]>    <chr [14]>    <chr [14]>     
##  9 996120f9-e84… A human single cell… <chr [1]>    <chr [1]>     <chr [1]>      
## 10 d7845650-f6b… A molecular single-… <chr [1]>    <chr [1]>     <chr [1]>      
## # … with 155 more rows

Use 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: 56 × 5
##    projectId     projectTitle         genusSpecies samples.organ specimens.organ
##    <chr>         <chr>                <list>       <list>        <list>         
##  1 53c53cd4-812… A Cellular Anatomy … <chr [1]>    <chr [1]>     <chr [1]>      
##  2 7027adc6-c9c… A Cellular Atlas of… <chr [1]>    <chr [1]>     <chr [1]>      
##  3 c1810dbc-16d… A cell atlas of hum… <chr [2]>    <chr [2]>     <chr [2]>      
##  4 a9301beb-e9f… A human cell atlas … <chr [1]>    <chr [14]>    <chr [14]>     
##  5 996120f9-e84… A human single cell… <chr [1]>    <chr [1]>     <chr [1]>      
##  6 842605c7-375… A single cell atlas… <chr [1]>    <chr [1]>     <chr [1]>      
##  7 a004b150-1c3… A single-cell atlas… <chr [1]>    <chr [1]>     <chr [1]>      
##  8 4a95101c-9ff… A single-cell refer… <chr [1]>    <chr [4]>     <chr [4]>      
##  9 1cd1f41f-f81… A single-cell surve… <chr [1]>    <chr [1]>     <chr [1]>      
## 10 8185730f-411… A single-cell trans… <chr [1]>    <chr [1]>     <chr [1]>      
## # … with 46 more rows

Use standard R commands to further filter projects to the one we are interested in, with title starting with “Single…”. Extract the unique projectId for this project.

project_tibble %>%
    filter(startsWith(projectTitle, "Single")) %>%
    t()
##                 [,1]                                               
## projectId       "0c3b7785-f74d-4091-8616-a68757e4c2a8"             
## projectTitle    "Single cell RNA sequencing of multiple myeloma II"
## genusSpecies    "Homo sapiens"                                     
## samples.organ   "hematopoietic system"                             
## specimens.organ "hematopoietic system"                             
##                 [,2]                                                                             
## projectId       "7b947aa2-43a7-4082-afff-222a3e3a4635"                                           
## projectTitle    "Single cell RNA-Seq of E18.5 developing mouse kidney and human kidney organoids"
## genusSpecies    character,2                                                                      
## samples.organ   "whole embryos"                                                                  
## specimens.organ character,2                                                                      
##                 [,3]                                                                                                             
## projectId       "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"                                                                                                         
##                 [,4]                                                                                           
## projectId       "b51f49b4-0d2e-4cbd-bbd5-04cd171fc2fa"                                                         
## projectTitle    "Single-cell RNA Sequencing of human microglia from post mortem Alzheimers Disease CNS tissue."
## genusSpecies    "Homo sapiens"                                                                                 
## samples.organ   "brain"                                                                                        
## specimens.organ "brain"                                                                                        
##                 [,5]                                               
## projectId       "2ef3655a-973d-4d69-9b41-21fa4041eed7"             
## projectTitle    "Single-cell RNA sequencing of normal human kidney"
## genusSpecies    "Homo sapiens"                                     
## samples.organ   "kidney"                                           
## specimens.organ "kidney"                                           
##                 [,6]                                                                                           
## projectId       "559bb888-7829-41f2-ace5-2c05c7eb81e9"                                                         
## projectTitle    "Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human."
## genusSpecies    "Homo sapiens"                                                                                 
## samples.organ   character,3                                                                                    
## specimens.organ character,3                                                                                    
##                 [,7]                                                                                       
## projectId       "4bec484d-ca7a-47b4-8d48-8830e06ad6db"                                                     
## projectTitle    "Single-cell RNA-Seq Investigation of Foveal and Peripheral Expression in the Human Retina"
## genusSpecies    "Homo sapiens"                                                                             
## samples.organ   "retina"                                                                                   
## specimens.organ "retina"                                                                                   
##                 [,8]                                                     
## 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"                                                  
##                 [,9]                                                                                                             
## projectId       "9d97f01f-9313-416e-9b07-560f048b2350"                                                                           
## projectTitle    "Single-cell RNA-sequencing of skin, fresh blood, and cultured peripheral blood mononuclear cells fr" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   character,2                                                                                                      
## specimens.organ character,2                                                                                                      
##                 [,10]                                                                                                            
## 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"                                                                                                           
##                 [,11]                                                                                                            
## projectId       "07073c12-8006-4710-a00b-23abdb814904"                                                                           
## projectTitle    "Single-cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expressio" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "blood vessel"                                                                                                   
## specimens.organ "blood vessel"                                                                                                   
##                 [,12]                                                                                    
## projectId       "962bd805-eb89-4c54-bad2-008e497d1307"                                                   
## projectTitle    "Single-cell analysis reveals congruence between kidney organoids and human fetal kidney"
## genusSpecies    "Homo sapiens"                                                                           
## samples.organ   character,0                                                                              
## specimens.organ "skin of body"                                                                           
##                 [,13]                                                                                                            
## projectId       "5ee710d7-e2d5-4fe2-818d-15f5e31dae32"                                                                           
## projectTitle    "Single-cell survey of human lymphatics unveils marked endothelial cell heterogeneity and mechanisms" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "lymph node"                                                                                                     
## specimens.organ "lymph node"                                                                                                     
##                 [,14]                                                                    
## projectId       "a39728aa-70a0-4201-b0a2-81b7badf3e71"                                   
## projectTitle    "Single-cell transcriptional profiles in human and mouse skeletal muscle"
## genusSpecies    character,2                                                              
## samples.organ   "skeletal muscle organ"                                                  
## specimens.organ "skeletal muscle organ"                                                  
##                 [,15]                                                                                                            
## projectId       "24c654a5-caa5-440a-8f02-582921f2db4a"                                                                           
## projectTitle    "Single-cell transcriptomics uncovers human corneal limbal stem cells and their differentiation traj" [truncated]
## genusSpecies    "Homo sapiens"                                                                                                   
## samples.organ   "eye"                                                                                                            
## specimens.organ "eye"                                                                                                            
##                 [,16]                                                                          
## projectId       "ce7b12ba-664f-4f79-8fc7-3de6b1892183"                                         
## projectTitle    "Single-nucleus RNA sequencing of human cortex affected by multiple sclerosis."
## genusSpecies    "Homo sapiens"                                                                 
## samples.organ   "brain"                                                                        
## specimens.organ "brain"

projectIds <-
    project_tibble %>%
    filter(startsWith(projectTitle, "Single")) %>%
    dplyr::pull(projectId)

projectId <- projectIds[1]

2.2 Discover and download the loom file of interest

files() retrieves (the first 1000) files from the Human Cell Atlas data portal. Construct a filter to restrict the files to loom files from the project we are interested in.

file_filter <- filters(
    projectId = list(is = projectId),
    fileFormat = list(is = "loom")
)

# only the two smallest files
file_tibble <- files(file_filter, size = 2, sort = "fileSize", order = "asc")

file_tibble
## # A tibble: 2 × 8
##   fileId   name     fileFormat    size version projectTitle  projectId  url     
##   <chr>    <chr>    <chr>        <int> <chr>   <chr>         <chr>      <chr>   
## 1 fe214fe… bone-ma… loom        4.04e7 2021-0… Single cell … 0c3b7785-… https:/…
## 2 e8136d6… 800cab7… loom        7.41e8 2021-0… Single cell … 0c3b7785-… https:/…

files_download() will download one or more files (one for each row) in file_tibble. The download is more complicated than simply following the url column of file_tibble, so it is not possible to simply copy the url into a browser. We’ll download the file and then immediately import it into R.

file_locations <- file_tibble %>% files_download()

LoomExperiment::import(unname(file_locations[1]),
                       type ="SingleCellLoomExperiment")
## class: SingleCellLoomExperiment 
## dim: 58347 3762 
## metadata(15): last_modified CreationDate ...
##   project.provenance.document_id specimen_from_organism.organ
## assays(1): matrix
## rownames: NULL
## rowData names(29): Gene antisense_reads ... reads_per_molecule
##   spliced_reads
## colnames: NULL
## colData names(43): CellID antisense_reads ... reads_unmapped
##   spliced_reads
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowGraphs(0): NULL
## colGraphs(0): NULL

Note that files_download() uses [BiocFileCache][https://bioconductor.org/packages/BiocFileCache], so individual files are only downloaded once.

3 Example: Illustrating access to h5ad files

This 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.

3.1 Projects facets and terms

The first challenge is to understand what file formats are available from the HCA. Obtain a tibble describing the ‘facets’ of the data, the number of terms used in each facet, and the number of distinct values used to describe projects.

projects_facets()
## # A tibble: 35 × 3
##    facet              n_terms n_values
##    <chr>                <int>    <int>
##  1 assayType                1      165
##  2 biologicalSex            5      259
##  3 cellLineType             6      173
##  4 contactName           1421     1741
##  5 contentDescription      25      453
##  6 developmentStage        91      284
##  7 donorDisease           153      339
##  8 effectiveOrgan          86      266
##  9 fileFormat              29      497
## 10 fileSource              10      378
## # … with 25 more rows

Note the fileFormat facet, and repeat projects_facets() to discover detail about available file formats

projects_facets("fileFormat")
## # A tibble: 29 × 3
##    facet      term     count
##    <chr>      <chr>    <int>
##  1 fileFormat fastq.gz   147
##  2 fileFormat loom        56
##  3 fileFormat bam         55
##  4 fileFormat tar         45
##  5 fileFormat txt.gz      28
##  6 fileFormat csv         25
##  7 fileFormat tsv.gz      19
##  8 fileFormat mtx.gz      17
##  9 fileFormat zip         14
## 10 fileFormat csv.gz      13
## # … with 19 more rows

Note that there are 8 uses of the h5ad file format. Use this as a filter to discover relevant projects.

filters <- filters(fileFormat = list(is = "h5ad"))
projects(filters)
## # A tibble: 10 × 5
##    projectId     projectTitle         genusSpecies samples.organ specimens.organ
##    <chr>         <chr>                <list>       <list>        <list>         
##  1 c1810dbc-16d… A cell atlas of hum… <chr [2]>    <chr [2]>     <chr [2]>      
##  2 ad98d3cd-26f… Cells of the adult … <chr [1]>    <chr [1]>     <chr [1]>      
##  3 83f5188e-3bf… Distinct microbial … <chr [1]>    <chr [2]>     <chr [2]>      
##  4 c4077b3c-5c9… Ischaemic sensitivi… <chr [1]>    <chr [3]>     <chr [3]>      
##  5 091cf39b-01b… Profiling of CD34+ … <chr [1]>    <chr [0]>     <chr [1]>      
##  6 f83165c5-e2e… Reconstructing the … <chr [1]>    <chr [3]>     <chr [3]>      
##  7 abe1a013-af7… Spatio-temporal imm… <chr [1]>    <chr [1]>     <chr [1]>      
##  8 b963bd4b-4bc… The cellular immune… <chr [1]>    <chr [1]>     <chr [1]>      
##  9 4e6f083b-5b9… The emergent landsc… <chr [1]>    <chr [3]>     <chr [3]>      
## 10 455b46e6-d8e… Transcriptomic char… <chr [1]>    <chr [3]>     <chr [3]>

3.2 Projects columns

The default tibble produced by projects() contains only some of the information available; the information is much richer.

To obtain a tibble with an expanded set of columns, you can specify that using the as parameter set to "tibble_expanded".

# an expanded set of columns for all or the first 4 projects
projects(as = 'tibble_expanded', size = 4)
## # A tibble: 4 × 81
##   projectId  cellSuspensions… cellSuspensions… cellSuspensions… cellSuspensions…
##   <chr>      <list>           <chr>            <list>           <chr>           
## 1 74b6d569-… <chr [1]>        brain            <chr [1]>        2019-05-16T16:0…
## 2 53c53cd4-… <chr [2]>        prostate gland   <chr [7]>        2021-05-13T22:1…
## 3 7027adc6-… <chr [0]>        heart            <chr [0]>        2020-08-04T10:4…
## 4 60ea42e1-… <chr [1]>        oral cavity      <chr [1]>        2021-05-19T16:5…
## # … with 76 more variables: cellSuspensions.totalCells <int>,
## #   cellSuspensions.updateDate <chr>, donorOrganisms.biologicalSex <chr>,
## #   donorOrganisms.developmentStage <list>, donorOrganisms.disease <chr>,
## #   donorOrganisms.donorCount <int>, donorOrganisms.genusSpecies <chr>,
## #   donorOrganisms.id <list>, donorOrganisms.organismAgeRange.gte <list>,
## #   donorOrganisms.organismAgeRange.lte <list>,
## #   donorOrganisms.organismAge.unit <list>, …

In the next sections, we’ll cover other options for the as parameter, and the data formats they return.

3.2.1 projects() as an R list

Instead 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 
##        165          8         36

hits 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                 2

shows 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]])
##          submissionDate              updateDate               projectId 
##                       1                       1                       1 
##            projectTitle        projectShortname              laboratory 
##                       1                       1                       1 
##      estimatedCellCount aggregateSubmissionDate     aggregateUpdateDate 
##                       0                       1                       1 
##      projectDescription            contributors            publications 
##                       1                       6                       1 
##  arrayExpressAccessions     geoSeriesAccessions  insdcProjectAccessions 
##                       1                       1                       1 
##    insdcStudyAccessions      supplementaryLinks                matrices 
##                       1                       1                       0 
##     contributorMatrices              accessions              accessible 
##                       1                       3                       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.

3.2.2 projects() as an lol

Use 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: 10387
## # total number of elements: 85535
## # number of leaf paths: 8179
## # number of leaf elements: 63952
## # lol_path():
## # A tibble: 10,387 × 3
##    path                                     n is_leaf
##    <chr>                                <int> <lgl>  
##  1 hits                                     1 FALSE  
##  2 hits[*]                                165 FALSE  
##  3 hits[*].cellLines                      165 FALSE  
##  4 hits[*].cellLines[*]                    22 FALSE  
##  5 hits[*].cellLines[*].cellLineType       22 FALSE  
##  6 hits[*].cellLines[*].cellLineType[*]    30 TRUE   
##  7 hits[*].cellLines[*].id                 22 FALSE  
##  8 hits[*].cellLines[*].id[*]             202 TRUE   
##  9 hits[*].cellLines[*].modelOrgan         22 FALSE  
## 10 hits[*].cellLines[*].modelOrgan[*]      34 TRUE   
## # … with 10,377 more rows

Use 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: 10255
## # total number of elements: 46351
## # number of leaf paths: 8111
## # number of leaf elements: 36977
## # lol_path():
## # A tibble: 10,255 × 3
##    path                                              n is_leaf
##    <chr>                                         <int> <lgl>  
##  1 hits[*].projects[*]                             165 FALSE  
##  2 hits[*].projects[*].accessible                  165 TRUE   
##  3 hits[*].projects[*].accessions                  165 FALSE  
##  4 hits[*].projects[*].accessions[*]               450 FALSE  
##  5 hits[*].projects[*].accessions[*].accession     450 TRUE   
##  6 hits[*].projects[*].accessions[*].namespace     450 TRUE   
##  7 hits[*].projects[*].aggregateSubmissionDate     165 TRUE   
##  8 hits[*].projects[*].aggregateUpdateDate         165 TRUE   
##  9 hits[*].projects[*].arrayExpressAccessions      165 FALSE  
## 10 hits[*].projects[*].arrayExpressAccessions[*]   171 TRUE   
## # … with 10,245 more rows
lol_select(lol, "hits[*].projects[*]") |>
    lol_filter(n == 44, is_leaf)
## # class: lol_hca lol
## # number of distinct paths: 0
## # total number of elements: 0
## # number of leaf paths: 0
## # number of leaf elements: 0
## # lol_path():
## # A tibble: 0 × 3
## # … with 3 variables: path <chr>, n <int>, is_leaf <lgl>

lol_pull() extracts a path from the lol as a vector; lol_lpull() extracts paths as lists.

titles <- lol_pull(lol, "hits[*].projects[*].projectTitle")
length(titles)
## [1] 165
head(titles, 2)
## [1] "1.3 Million Brain Cells from E18 Mice"                                      
## [2] "A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra"

3.2.3 Creating projects() tibbles with specific columns

The path or its abbreviation can be used to specify the columns of the tibble to be returned by the projects() query.

Here we retrieve additional details of donor count and total cells by adding appropriate path abbreviations to a named character vector. Names on the character vector can be used to rename the path more concisely, but the paths must uniquely identify elements in the list-of-lists.

columns <- c(
    projectId = "hits[*].entryId",
    projectTitle = "hits[*].projects[*].projectTitle",
    genusSpecies = "hits[*].donorOrganisms[*].genusSpecies[*]",
    donorCount = "hits[*].donorOrganisms[*].donorCount",
    cellSuspensions.organ = "hits[*].cellSuspensions[*].organ[*]",
    totalCells = "hits[*].cellSuspensions[*].totalCells"
)
projects <- projects(filters, columns = columns)
projects
## # A tibble: 10 × 6
##    projectId  projectTitle   genusSpecies donorCount cellSuspensions… totalCells
##    <chr>      <chr>          <list>            <int> <list>           <list>    
##  1 c1810dbc-… A cell atlas … <chr [2]>            24 <chr [2]>        <int [2]> 
##  2 ad98d3cd-… Cells of the … <chr [1]>            14 <chr [1]>        <int [1]> 
##  3 83f5188e-… Distinct micr… <chr [1]>             6 <chr [2]>        <int [2]> 
##  4 c4077b3c-… Ischaemic sen… <chr [1]>            14 <chr [3]>        <int [3]> 
##  5 091cf39b-… Profiling of … <chr [1]>             3 <chr [1]>        <int [1]> 
##  6 f83165c5-… Reconstructin… <chr [1]>            16 <chr [3]>        <int [0]> 
##  7 abe1a013-… Spatio-tempor… <chr [1]>             8 <chr [1]>        <int [0]> 
##  8 b963bd4b-… The cellular … <chr [1]>           120 <chr [1]>        <int [1]> 
##  9 4e6f083b-… The emergent … <chr [1]>             6 <chr [3]>        <int [3]> 
## 10 455b46e6-… Transcriptomi… <chr [1]>             4 <chr [3]>        <int [3]>

Note that the cellSuspensions.organ and totalCells columns have more than one entry per project.

projects |>
   select(projectId, cellSuspensions.organ, totalCells)
## # A tibble: 10 × 3
##    projectId                            cellSuspensions.organ totalCells
##    <chr>                                <list>                <list>    
##  1 c1810dbc-16d2-45c3-b45e-3e675f88d87b <chr [2]>             <int [2]> 
##  2 ad98d3cd-26fb-4ee3-99c9-8a2ab085e737 <chr [1]>             <int [1]> 
##  3 83f5188e-3bf7-4956-9544-cea4f8997756 <chr [2]>             <int [2]> 
##  4 c4077b3c-5c98-4d26-a614-246d12c2e5d7 <chr [3]>             <int [3]> 
##  5 091cf39b-01bc-42e5-9437-f419a66c8a45 <chr [1]>             <int [1]> 
##  6 f83165c5-e2ea-4d15-a5cf-33f3550bffde <chr [3]>             <int [0]> 
##  7 abe1a013-af7a-45ed-8c26-f3793c24a1f4 <chr [1]>             <int [0]> 
##  8 b963bd4b-4bc1-4404-8425-69d74bc636b8 <chr [1]>             <int [1]> 
##  9 4e6f083b-5b9a-4393-9890-2a83da8188f1 <chr [3]>             <int [3]> 
## 10 455b46e6-d8ea-4611-861e-de720a562ada <chr [3]>             <int [3]>

In this case, the mapping between cellSuspensions.organ and totalCells is clear, but in general more refined navigation of the lol structure may be necessary.

projects |>
    select(projectId, cellSuspensions.organ, totalCells) |>
    filter(lengths(totalCells) > 0) |>
    tidyr::unnest(c("cellSuspensions.organ", "totalCells"))
## # A tibble: 16 × 3
##    projectId                            cellSuspensions.organ totalCells
##    <chr>                                <chr>                      <int>
##  1 c1810dbc-16d2-45c3-b45e-3e675f88d87b thymus                    456000
##  2 c1810dbc-16d2-45c3-b45e-3e675f88d87b colon                      16000
##  3 ad98d3cd-26fb-4ee3-99c9-8a2ab085e737 heart                     791000
##  4 83f5188e-3bf7-4956-9544-cea4f8997756 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 spleen                     66553
##  8 c4077b3c-5c98-4d26-a614-246d12c2e5d7 lung                       40025
##  9 091cf39b-01bc-42e5-9437-f419a66c8a45 hematopoietic system     1480000
## 10 b963bd4b-4bc1-4404-8425-69d74bc636b8 blood                     800000
## 11 4e6f083b-5b9a-4393-9890-2a83da8188f1 presumptive gut            30952
## 12 4e6f083b-5b9a-4393-9890-2a83da8188f1 endoderm                   54166
## 13 4e6f083b-5b9a-4393-9890-2a83da8188f1 embryo                     27083
## 14 455b46e6-d8ea-4611-861e-de720a562ada spleen                     60043
## 15 455b46e6-d8ea-4611-861e-de720a562ada bone marrow                87532
## 16 455b46e6-d8ea-4611-861e-de720a562ada blood                      25016

Select the following entry, augment the filter, and query available files

projects %>%
    filter(startsWith(projectTitle, "Reconstruct")) %>%
    t()
##                       [,1]                                                                                                 
## projectId             "f83165c5-e2ea-4d15-a5cf-33f3550bffde"                                                               
## projectTitle          "Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics"
## genusSpecies          "Homo sapiens"                                                                                       
## donorCount            16                                                                                                   
## cellSuspensions.organ character,3                                                                                          
## totalCells            integer,0

This approach can be used to customize the tibbles returned by the other main functions in the package, files(), samples(), and bundles().

3.3 File download

The relevant file can be selected and downloaded using the technique in the first example.

filters <- filters(
    projectId = list(is = "f83165c5-e2ea-4d15-a5cf-33f3550bffde"),
    fileFormat = list(is = "h5ad")
)
files <-
    files(filters) %>%
    head(1)            # only first file, for demonstration
files %>% t()
##              [,1]                                                                                                                                                      
## fileId       "6d4fedcf-857d-5fbb-9928-8b9605500a69"                                                                                                                    
## name         "vento18_ss2.processed.h5ad"                                                                                                                              
## fileFormat   "h5ad"                                                                                                                                                    
## size         "82121633"                                                                                                                                                
## version      "2021-02-10T16:56:40.419579Z"                                                                                                                             
## projectTitle "Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics"                                                     
## projectId    "f83165c5-e2ea-4d15-a5cf-33f3550bffde"                                                                                                                    
## url          "https://service.azul.data.humancellatlas.org/repository/files/6d4fedcf-857d-5fbb-9928-8b9605500a69?catalog=dcp10&version=2021-02-10T16%3A56%3A40.419579Z"
file_path <- files_download(files)

"h5ad" files can be read as SingleCellExperiment objects using the zellkonverter package.

## don't want large amount of data read from disk
sce <- zellkonverter::readH5AD(file_path, use_hdf5 = TRUE)
sce

4 Example: A multiple file download

project_filter <- filters(fileFormat = list(is = "csv"))
project_tibble <- projects(project_filter)

project_tibble %>%
    filter(
        startsWith(
            projectTitle,
            "Reconstructing the human first trimester"
        )
    )
## # A tibble: 1 × 5
##   projectId     projectTitle          genusSpecies samples.organ specimens.organ
##   <chr>         <chr>                 <list>       <list>        <list>         
## 1 f83165c5-e2e… Reconstructing the h… <chr [1]>    <chr [3]>     <chr [3]>

projectId <-
    project_tibble %>%
    filter(
        startsWith(
            projectTitle,
            "Reconstructing the human first trimester"
        )
    ) %>%
    pull(projectId)

file_filter <- filters(
    projectId = list(is = projectId),
    fileFormat = list(is = "csv")
)

## first 4 files will be returned
file_tibble <- files(file_filter, size = 4)

file_tibble %>%
    files_download()
## 7f9a181e-24c5-5462-b308-7fef5b1bda2a-2021-02-10T16:56:40.419579Z 
## "/home/biocbuild/.cache/R/hca/2702d06362079e_2702d06362079e.csv" 
## d04c6e3c-b740-5586-8420-4480a1b5706c-2021-02-10T16:56:40.419579Z 
## "/home/biocbuild/.cache/R/hca/2702d036ed90a2_2702d036ed90a2.csv" 
## d30ffc0b-7d6e-5b85-aff9-21ec69663a81-2021-02-10T16:56:40.419579Z 
## "/home/biocbuild/.cache/R/hca/2702d0686bf175_2702d0686bf175.csv" 
## e1517725-01b0-5346-9788-afca63e9993a-2021-02-10T16:56:40.419579Z 
##   "/home/biocbuild/.cache/R/hca/2702d0208cf3d_2702d0208cf3d.csv"

5 Example: Exploring the pagination feature

The files(), bundles(), and samples() can all return many 1000’s of results. It is necessary to ‘page’ through these to see all of them. We illustrate pagination with projects(), retrieving only 30 projects.

Pagination works for the default tibble output

page_1_tbl <- projects(size = 30)
page_1_tbl
## # A tibble: 30 × 5
##    projectId     projectTitle         genusSpecies samples.organ specimens.organ
##    <chr>         <chr>                <list>       <list>        <list>         
##  1 74b6d569-3b1… 1.3 Million Brain C… <chr [1]>    <chr [1]>     <chr [1]>      
##  2 53c53cd4-812… A Cellular Anatomy … <chr [1]>    <chr [1]>     <chr [1]>      
##  3 7027adc6-c9c… A Cellular Atlas of… <chr [1]>    <chr [1]>     <chr [1]>      
##  4 60ea42e1-af4… A Protocol for Reve… <chr [1]>    <chr [1]>     <chr [1]>      
##  5 f86f1ab4-1fb… A Single-Cell Trans… <chr [2]>    <chr [1]>     <chr [1]>      
##  6 602628d7-c03… A Single-cell Trans… <chr [1]>    <chr [3]>     <chr [3]>      
##  7 c1810dbc-16d… A cell atlas of hum… <chr [2]>    <chr [2]>     <chr [2]>      
##  8 a9301beb-e9f… A human cell atlas … <chr [1]>    <chr [14]>    <chr [14]>     
##  9 996120f9-e84… A human single cell… <chr [1]>    <chr [1]>     <chr [1]>      
## 10 d7845650-f6b… A molecular single-… <chr [1]>    <chr [1]>     <chr [1]>      
## # … with 20 more rows

page_2_tbl <- page_1_tbl %>% hca_next()
page_2_tbl
## # A tibble: 30 × 5
##    projectId     projectTitle         genusSpecies samples.organ specimens.organ
##    <chr>         <chr>                <list>       <list>        <list>         
##  1 c893cb57-5c9… Colonic single epit… <chr [1]>    <chr [1]>     <chr [1]>      
##  2 16ed4ad8-731… Comparative analysi… <chr [1]>    <chr [1]>     <chr [1]>      
##  3 8787c238-89e… Comparison of manua… <chr [1]>    <chr [0]>     <chr [1]>      
##  4 a9c022b4-c77… Comparison, calibra… <chr [1]>    <chr [0]>     <chr [1]>      
##  5 79b13a2a-9ca… Comprehensive singl… <chr [1]>    <chr [1]>     <chr [1]>      
##  6 f2fe82f0-445… Decoding the develo… <chr [1]>    <chr [4]>     <chr [4]>      
##  7 b4a7d12f-6c2… Defining the Activa… <chr [1]>    <chr [1]>     <chr [1]>      
##  8 c5f46615-68d… Developmental cell … <chr [1]>    <chr [1]>     <chr [1]>      
##  9 2a64db43-1b5… Direct exposure to … <chr [1]>    <chr [1]>     <chr [1]>      
## 10 8a40ff19-e61… Dissecting the Glob… <chr [1]>    <chr [1]>     <chr [1]>      
## # … with 20 more rows

## should be identical to page_1_tbl
page_2_tbl %>% hca_prev()
## # A tibble: 30 × 5
##    projectId     projectTitle         genusSpecies samples.organ specimens.organ
##    <chr>         <chr>                <list>       <list>        <list>         
##  1 74b6d569-3b1… 1.3 Million Brain C… <chr [1]>    <chr [1]>     <chr [1]>      
##  2 53c53cd4-812… A Cellular Anatomy … <chr [1]>    <chr [1]>     <chr [1]>      
##  3 7027adc6-c9c… A Cellular Atlas of… <chr [1]>    <chr [1]>     <chr [1]>      
##  4 60ea42e1-af4… A Protocol for Reve… <chr [1]>    <chr [1]>     <chr [1]>      
##  5 f86f1ab4-1fb… A Single-Cell Trans… <chr [2]>    <chr [1]>     <chr [1]>      
##  6 602628d7-c03… A Single-cell Trans… <chr [1]>    <chr [3]>     <chr [3]>      
##  7 c1810dbc-16d… A cell atlas of hum… <chr [2]>    <chr [2]>     <chr [2]>      
##  8 a9301beb-e9f… A human cell atlas … <chr [1]>    <chr [14]>    <chr [14]>     
##  9 996120f9-e84… A human single cell… <chr [1]>    <chr [1]>     <chr [1]>      
## 10 d7845650-f6b… A molecular single-… <chr [1]>    <chr [1]>     <chr [1]>      
## # … with 20 more rows

Pagination also works for the lol objects

page_1_lol <- projects(size = 5, as = "lol")
page_1_lol %>%
    lol_pull("hits[*].projects[*].projectTitle")
## [1] "1.3 Million Brain Cells from E18 Mice"                                                                              
## [2] "A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra"                                        
## [3] "A Cellular Atlas of Pitx2-Dependent Cardiac Development."                                                           
## [4] "A Protocol for Revealing Oral Neutrophil Heterogeneity by Single-Cell Immune Profiling in Human Saliva"             
## [5] "A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure"

page_2_lol <-
    page_1_lol %>%
    hca_next()
page_2_lol %>%
    lol_pull("hits[*].projects[*].projectTitle")
## [1] "A Single-cell Transcriptomic Atlas of Human Intervertebral Disc"                                                                                                               
## [2] "A cell atlas of human thymic development defines T cell repertoire formation"                                                                                                  
## [3] "A human cell atlas of fetal gene expression."                                                                                                                                  
## [4] "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."
## [5] "A molecular single-cell lung atlas of lethal COVID-19"

## should be identical to page_1_lol
page_2_lol %>%
    hca_prev() %>%
    lol_pull("hits[*].projects[*].projectTitle")
## [1] "1.3 Million Brain Cells from E18 Mice"                                                                              
## [2] "A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra"                                        
## [3] "A Cellular Atlas of Pitx2-Dependent Cardiac Development."                                                           
## [4] "A Protocol for Revealing Oral Neutrophil Heterogeneity by Single-Cell Immune Profiling in Human Saliva"             
## [5] "A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure"

6 Example: Obtaining other data entities

Much like projects() and files(), samples() and bundles() allow you to provide a filter object and additional criteria to retrieve data in the form of samples and bundles respectively

heart_filters <- filters(organ = list(is = "heart"))
heart_samples <- samples(filters = heart_filters, size = 4)
heart_samples
## # A tibble: 4 × 6
##   entryId          projectTitle              genusSpecies disease fileType count
##   <chr>            <chr>                     <chr>        <chr>   <chr>    <int>
## 1 012c52ff-4770-4… A Cellular Atlas of Pitx… Mus musculus normal  fastq.gz     2
## 2 035db5b9-a219-4… A Cellular Atlas of Pitx… Mus musculus normal  fastq.gz     2
## 3 09e425f7-22d7-4… A Cellular Atlas of Pitx… Mus musculus normal  fastq.gz     2
## 4 2273e44d-9fbc-4… A Cellular Atlas of Pitx… Mus musculus normal  fastq.gz     2

heart_bundles <- bundles(filters = heart_filters, size = 4)
heart_bundles
## # A tibble: 4 × 6
##   projectTitle        genusSpecies samples  files bundleUuid     bundleVersion  
##   <chr>               <chr>        <list>   <lis> <chr>          <chr>          
## 1 A Cellular Atlas o… Mus musculus <chr [2… <chr… 0d391bd1-92a9… 2021-02-26T01:…
## 2 A Cellular Atlas o… Mus musculus <chr [1… <chr… 165a2df1-07a0… 2021-02-26T01:…
## 3 A Cellular Atlas o… Mus musculus <chr [2… <chr… 166c1b1a-ad9c… 2020-08-04T10:…
## 4 A Cellular Atlas o… Mus musculus <chr [1… <chr… 18bad6b1-c55d… 2021-02-26T01:…

7 Example: Obtaining summaries of project catalogs

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: 5 × 3
##   fileType count     totalSize
##   <chr>    <int>         <dbl>
## 1 fastq.gz 28225 4690836890519
## 2 loom       169  355865926256
## 3 bam        164 3284598129743
## 4 RDS          3     301293176
## 5 Rds          3    2637887113
first_catalog <- catalogs()[1]
summary(type = "overview", catalog = first_catalog)
## # A tibble: 9 × 2
##   name                        value
##   <chr>                       <dbl>
## 1 projectCount              1.65e 2
## 2 specimenCount             9.10e 3
## 3 speciesCount              3   e 0
## 4 fileCount                 3.59e 5
## 5 totalFileSize             1.06e14
## 6 donorCount                1.97e 3
## 7 labCount                  3.1 e 2
## 8 totalCellCount            1.99e 7
## 9 projectEstimatedCellCount 6.33e 5

8 Example: Obtaining details on individual projects, files, samples, and bundles

Each project, file, sample, and bundles has its own unique ID by which, in conjunction with its catalog, can be to uniquely identify them.

heart_filters <- filters(organ = list(is = "heart"))
heart_projects <- projects(filters = heart_filters, size = 4)
heart_projects
## # A tibble: 4 × 5
##   projectId     projectTitle          genusSpecies samples.organ specimens.organ
##   <chr>         <chr>                 <chr>        <list>        <list>         
## 1 7027adc6-c9c… A Cellular Atlas of … Mus musculus <chr [1]>     <chr [1]>      
## 2 a9301beb-e9f… A human cell atlas o… Homo sapiens <chr [14]>    <chr [14]>     
## 3 ad98d3cd-26f… Cells of the adult h… Homo sapiens <chr [1]>     <chr [1]>      
## 4 bd400331-54b… Sex-Specific Control… Homo sapiens <chr [1]>     <chr [1]>

projectId <-
    heart_projects %>%
    filter(
        startsWith(
            projectTitle,
            "Cells of the adult human"
        )
    ) %>%
    dplyr::pull(projectId)

projects_detail(uuid = projectId)
## $protocols
## $protocols[[1]]
## $protocols[[1]]$submissionDate
## [1] "2021-02-26T16:30:00.000000Z"
## 
## $protocols[[1]]$updateDate
## [1] "2021-05-24T12:00:00.000000Z"
## 
## $protocols[[1]]$workflow
## $protocols[[1]]$workflow[[1]]
## [1] "optimus_post_processing_v1.0.0"
## 
## $protocols[[1]]$workflow[[2]]
## [1] "optimus_v4.2.2"
## 
## 
## 
## $protocols[[2]]
## $protocols[[2]]$submissionDate
## [1] "2020-07-24T16:39:01.987000Z"
## 
## $protocols[[2]]$updateDate
## [1] "2020-07-24T16:39:11.033000Z"
## 
## $protocols[[2]]$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]]
## $protocols[[3]]$submissionDate
## [1] "2020-07-24T16:39:02.027000Z"
## 
## $protocols[[3]]$updateDate
## [1] "2020-07-24T16:39:11.288000Z"
## 
## $protocols[[3]]$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] "1cbf0879-2471-4a8c-bb41-c71d1693021e"
## 
## $sources[[1]]$sourceSpec
## [1] "tdr:tdr-fp-43194825:snapshot/hca_prod_20201120_dcp2___20211004_dcp10:/2"
## 
## 
## 
## $projects
## $projects[[1]]
## $projects[[1]]$submissionDate
## [1] "2020-07-22T12:26:56.289000Z"
## 
## $projects[[1]]$updateDate
## [1] "2020-10-19T16:31:10.620000Z"
## 
## $projects[[1]]$projectId
## [1] "ad98d3cd-26fb-4ee3-99c9-8a2ab085e737"
## 
## $projects[[1]]$projectTitle
## [1] "Cells of the adult human heart"
## 
## $projects[[1]]$projectShortname
## [1] "HeartSingleCellsAndNucleiSeq"
## 
## $projects[[1]]$laboratory
## $projects[[1]]$laboratory[[1]]
## [1] "Cardiovascular Division"
## 
## $projects[[1]]$laboratory[[2]]
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$laboratory[[3]]
## [1] "Cellular Genetics"
## 
## $projects[[1]]$laboratory[[4]]
## [1] "Department of Genetics"
## 
## $projects[[1]]$laboratory[[5]]
## [1] "Department of Histology and Embryology of Zhongshan School of Medicine"
## 
## $projects[[1]]$laboratory[[6]]
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
## 
## $projects[[1]]$laboratory[[7]]
## [1] "Human Cell Atlas Data Coordination Platform"
## 
## $projects[[1]]$laboratory[[8]]
## [1] "Institute of Computational Biology (ICB)"
## 
## $projects[[1]]$laboratory[[9]]
## [1] "National Heart and Lung Institute"
## 
## 
## $projects[[1]]$estimatedCellCount
## NULL
## 
## $projects[[1]]$aggregateSubmissionDate
## [1] "2020-07-22T12:26:56.289000Z"
## 
## $projects[[1]]$aggregateUpdateDate
## [1] "2021-05-24T12:00:00.000000Z"
## 
## $projects[[1]]$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] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[1]]$contactName
## [1] "Kenny,,Roberts"
## 
## $projects[[1]]$contributors[[1]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[1]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[1]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[1]]$email
## [1] "kr19@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[2]]
## $projects[[1]]$contributors[[2]]$institution
## [1] "Imperial College London"
## 
## $projects[[1]]$contributors[[2]]$contactName
## [1] "Joseph,J.,Boyle"
## 
## $projects[[1]]$contributors[[2]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[2]]$laboratory
## [1] "National Heart and Lung Institute"
## 
## $projects[[1]]$contributors[[2]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[2]]$email
## [1] "joseph.boyle@imperial.ac.uk"
## 
## 
## $projects[[1]]$contributors[[3]]
## $projects[[1]]$contributors[[3]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[3]]$contactName
## [1] "Omer,,Bayraktar"
## 
## $projects[[1]]$contributors[[3]]$projectRole
## [1] "co-investigator"
## 
## $projects[[1]]$contributors[[3]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[3]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[3]]$email
## [1] "ob5@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[4]]
## $projects[[1]]$contributors[[4]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[4]]$contactName
## [1] "J.,G.,Seidman"
## 
## $projects[[1]]$contributors[[4]]$projectRole
## [1] "principal investigator"
## 
## $projects[[1]]$contributors[[4]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[4]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[4]]$email
## [1] "seidman@genetics.med.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[5]]
## $projects[[1]]$contributors[[5]]$institution
## [1] "University of Alberta"
## 
## $projects[[1]]$contributors[[5]]$contactName
## [1] "Gavin,,Oudit"
## 
## $projects[[1]]$contributors[[5]]$projectRole
## [1] "co-investigator"
## 
## $projects[[1]]$contributors[[5]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
## 
## $projects[[1]]$contributors[[5]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[5]]$email
## [1] "gavin.oudit@ualberta.ca"
## 
## 
## $projects[[1]]$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] "Masatoshi,,Kanda"
## 
## $projects[[1]]$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] "masatoshi.kanda@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[7]]
## $projects[[1]]$contributors[[7]]$institution
## [1] "University of Alberta"
## 
## $projects[[1]]$contributors[[7]]$contactName
## [1] "Anissa,,Viveiros"
## 
## $projects[[1]]$contributors[[7]]$projectRole
## [1] "biomaterial provider"
## 
## $projects[[1]]$contributors[[7]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
## 
## $projects[[1]]$contributors[[7]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[7]]$email
## [1] "aviveiro@ualberta.ca"
## 
## 
## $projects[[1]]$contributors[[8]]
## $projects[[1]]$contributors[[8]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[8]]$contactName
## [1] "Daniel,,Reichart"
## 
## $projects[[1]]$contributors[[8]]$projectRole
## [1] "lead analyst"
## 
## $projects[[1]]$contributors[[8]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[8]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[8]]$email
## [1] "Daniel_Reichart@hms.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[9]]
## $projects[[1]]$contributors[[9]]$institution
## [1] "Brigham and Women’s Hospital"
## 
## $projects[[1]]$contributors[[9]]$contactName
## [1] "Barbara,,McDonough"
## 
## $projects[[1]]$contributors[[9]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[9]]$laboratory
## [1] "Cardiovascular Division"
## 
## $projects[[1]]$contributors[[9]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[9]]$email
## [1] "mcdonough@genetics.med.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[10]]
## $projects[[1]]$contributors[[10]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[10]]$contactName
## [1] "Daniel,,DeLaughter"
## 
## $projects[[1]]$contributors[[10]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[10]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[10]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[10]]$email
## [1] "Daniel_DeLaughter@hms.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[11]]
## $projects[[1]]$contributors[[11]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
## 
## $projects[[1]]$contributors[[11]]$contactName
## [1] "Catherine,L.,Worth"
## 
## $projects[[1]]$contributors[[11]]$projectRole
## [1] "analyst"
## 
## $projects[[1]]$contributors[[11]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[11]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[11]]$email
## [1] "catherine.sargent@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[12]]
## $projects[[1]]$contributors[[12]]$institution
## [1] "EMBL-EBI"
## 
## $projects[[1]]$contributors[[12]]$contactName
## [1] "Marion,F,Shadbolt"
## 
## $projects[[1]]$contributors[[12]]$projectRole
## [1] "data curator"
## 
## $projects[[1]]$contributors[[12]]$laboratory
## [1] "Human Cell Atlas Data Coordination Platform"
## 
## $projects[[1]]$contributors[[12]]$correspondingContributor
## [1] FALSE
## 
## $projects[[1]]$contributors[[12]]$email
## [1] "mshadbolt@ebi.ac.uk"
## 
## 
## $projects[[1]]$contributors[[13]]
## $projects[[1]]$contributors[[13]]$institution
## [1] "Imperial College London"
## 
## $projects[[1]]$contributors[[13]]$contactName
## [1] "Sara,,Samari"
## 
## $projects[[1]]$contributors[[13]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[13]]$laboratory
## [1] "National Heart and Lung Institute"
## 
## $projects[[1]]$contributors[[13]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[13]]$email
## [1] "sara.samari13@imperial.ac.uk"
## 
## 
## $projects[[1]]$contributors[[14]]
## $projects[[1]]$contributors[[14]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[14]]$contactName
## [1] "Liz,,Tuck"
## 
## $projects[[1]]$contributors[[14]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[14]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[14]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[14]]$email
## [1] "et2@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[15]]
## $projects[[1]]$contributors[[15]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
## 
## $projects[[1]]$contributors[[15]]$contactName
## [1] "Eric,L.,Lindberg"
## 
## $projects[[1]]$contributors[[15]]$projectRole
## [1] "analyst"
## 
## $projects[[1]]$contributors[[15]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[15]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[15]]$email
## [1] "Eric.Lindberg@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[16]]
## $projects[[1]]$contributors[[16]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[16]]$contactName
## [1] "Hiroko,,Wakimoto"
## 
## $projects[[1]]$contributors[[16]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[16]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[16]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[16]]$email
## [1] "hwakimoto@genetics.med.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[17]]
## $projects[[1]]$contributors[[17]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[17]]$contactName
## [1] "Emily,,Nadelmann"
## 
## $projects[[1]]$contributors[[17]]$projectRole
## [1] "analyst"
## 
## $projects[[1]]$contributors[[17]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[17]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[17]]$email
## [1] "Emily_Nadelmann@hms.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[18]]
## $projects[[1]]$contributors[[18]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[18]]$contactName
## [1] "Eirini,S.,Fasouli"
## 
## $projects[[1]]$contributors[[18]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[18]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[18]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[18]]$email
## [1] "ef5@sanger.ac.uk"
## 
## 
## $projects[[1]]$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] "Giannino,,Patone"
## 
## $projects[[1]]$contributors[[19]]$projectRole
## [1] "computational scientist"
## 
## $projects[[1]]$contributors[[19]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[19]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[19]]$email
## [1] "Giannino.Patone@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[20]]
## $projects[[1]]$contributors[[20]]$institution
## [1] "Imperial College London"
## 
## $projects[[1]]$contributors[[20]]$contactName
## [1] "Michela,,Noseda"
## 
## $projects[[1]]$contributors[[20]]$projectRole
## [1] "principal investigator"
## 
## $projects[[1]]$contributors[[20]]$laboratory
## [1] "National Heart and Lung Institute"
## 
## $projects[[1]]$contributors[[20]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[20]]$email
## [1] "m.noseda@imperial.ac.uk"
## 
## 
## $projects[[1]]$contributors[[21]]
## $projects[[1]]$contributors[[21]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[21]]$contactName
## [1] "Krzysztof,,Polanski"
## 
## $projects[[1]]$contributors[[21]]$projectRole
## [1] "computational scientist"
## 
## $projects[[1]]$contributors[[21]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[21]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[21]]$email
## [1] "kp9@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[22]]
## $projects[[1]]$contributors[[22]]$institution
## [1] "Cambridge Biorepository for Translational Medicine"
## 
## $projects[[1]]$contributors[[22]]$contactName
## [1] "Kourosh,,Saeb-Parsy"
## 
## $projects[[1]]$contributors[[22]]$projectRole
## [1] "co-investigator"
## 
## $projects[[1]]$contributors[[22]]$laboratory
## NULL
## 
## $projects[[1]]$contributors[[22]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[22]]$email
## [1] "ks10014@cam.ac.uk"
## 
## 
## $projects[[1]]$contributors[[23]]
## $projects[[1]]$contributors[[23]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[23]]$contactName
## [1] "Sarah,A.,Teichmann"
## 
## $projects[[1]]$contributors[[23]]$projectRole
## [1] "principal investigator"
## 
## $projects[[1]]$contributors[[23]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[23]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[23]]$email
## [1] "st9@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[24]]
## $projects[[1]]$contributors[[24]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[24]]$contactName
## [1] "Monika,,Litviňuková"
## 
## $projects[[1]]$contributors[[24]]$projectRole
## [1] "lead analyst"
## 
## $projects[[1]]$contributors[[24]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[24]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[24]]$email
## [1] "monika.litvinukova@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[25]]
## $projects[[1]]$contributors[[25]]$institution
## [1] "Wellcome Sanger Institute"
## 
## $projects[[1]]$contributors[[25]]$contactName
## [1] "Carlos,,Talavera-López"
## 
## $projects[[1]]$contributors[[25]]$projectRole
## [1] "lead analyst"
## 
## $projects[[1]]$contributors[[25]]$laboratory
## [1] "Cellular Genetics"
## 
## $projects[[1]]$contributors[[25]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[25]]$email
## [1] "ct5@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[26]]
## $projects[[1]]$contributors[[26]]$institution
## [1] "University of Alberta"
## 
## $projects[[1]]$contributors[[26]]$contactName
## [1] "Hao,,Zhang"
## 
## $projects[[1]]$contributors[[26]]$projectRole
## [1] "biomaterial provider"
## 
## $projects[[1]]$contributors[[26]]$laboratory
## [1] "Division of Cardiology Faculty of Medicine and Dentistry"
## 
## $projects[[1]]$contributors[[26]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[26]]$email
## [1] "hzhang10@ualberta.ca"
## 
## 
## $projects[[1]]$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] "Norbert,,Hübner"
## 
## $projects[[1]]$contributors[[27]]$projectRole
## [1] "principal investigator"
## 
## $projects[[1]]$contributors[[27]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[27]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[27]]$email
## [1] "nhuebner@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[28]]
## $projects[[1]]$contributors[[28]]$institution
## [1] "HMGU"
## 
## $projects[[1]]$contributors[[28]]$contactName
## [1] "Matthias,,Heinig"
## 
## $projects[[1]]$contributors[[28]]$projectRole
## [1] "co-investigator"
## 
## $projects[[1]]$contributors[[28]]$laboratory
## [1] "Institute of Computational Biology (ICB)"
## 
## $projects[[1]]$contributors[[28]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[28]]$email
## [1] "matthias.heinig@helmholtz-muenchen.de"
## 
## 
## $projects[[1]]$contributors[[29]]
## $projects[[1]]$contributors[[29]]$institution
## [1] "Sun-Yat Sen University"
## 
## $projects[[1]]$contributors[[29]]$contactName
## [1] "Hongbo,,Zhang"
## 
## $projects[[1]]$contributors[[29]]$projectRole
## [1] "co-investigator"
## 
## $projects[[1]]$contributors[[29]]$laboratory
## [1] "Department of Histology and Embryology of Zhongshan School of Medicine"
## 
## $projects[[1]]$contributors[[29]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[29]]$email
## [1] "hz3@sanger.ac.uk"
## 
## 
## $projects[[1]]$contributors[[30]]
## $projects[[1]]$contributors[[30]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[30]]$contactName
## [1] "Joshua,M,Gorham"
## 
## $projects[[1]]$contributors[[30]]$projectRole
## [1] "experimental scientist"
## 
## $projects[[1]]$contributors[[30]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[30]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[30]]$email
## [1] "jgorham@genetics.med.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[31]]
## $projects[[1]]$contributors[[31]]$institution
## [1] "Cambridge Biorepository for Translational Medicine"
## 
## $projects[[1]]$contributors[[31]]$contactName
## [1] "Krishnaa,T.,Mahbubani"
## 
## $projects[[1]]$contributors[[31]]$projectRole
## [1] "biomaterial provider"
## 
## $projects[[1]]$contributors[[31]]$laboratory
## NULL
## 
## $projects[[1]]$contributors[[31]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[31]]$email
## [1] "ktam2@cam.ac.uk"
## 
## 
## $projects[[1]]$contributors[[32]]
## $projects[[1]]$contributors[[32]]$institution
## [1] "Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)"
## 
## $projects[[1]]$contributors[[32]]$contactName
## [1] "Henrike,,Maatz"
## 
## $projects[[1]]$contributors[[32]]$projectRole
## [1] "lead analyst"
## 
## $projects[[1]]$contributors[[32]]$laboratory
## [1] "Cardiovascular and Metabolic Sciences"
## 
## $projects[[1]]$contributors[[32]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[32]]$email
## [1] "h.maatz@mdc-berlin.de"
## 
## 
## $projects[[1]]$contributors[[33]]
## $projects[[1]]$contributors[[33]]$institution
## [1] "Harvard Medical School"
## 
## $projects[[1]]$contributors[[33]]$contactName
## [1] "Christine,,Seidman"
## 
## $projects[[1]]$contributors[[33]]$projectRole
## [1] "principal investigator"
## 
## $projects[[1]]$contributors[[33]]$laboratory
## [1] "Department of Genetics"
## 
## $projects[[1]]$contributors[[33]]$correspondingContributor
## [1] TRUE
## 
## $projects[[1]]$contributors[[33]]$email
## [1] "cseidman@genetics.med.harvard.edu"
## 
## 
## $projects[[1]]$contributors[[34]]
## $projects[[1]]$contributors[[34]]$institution
## [1] "Imperial College London"
## 
## $projects[[1]]$contributors[[34]]$contactName
## [1] "Michael,,Lee"
## 
## $projects[[1]]$contributors[[34]]$projectRole
## [1] "analyst"
## 
## $projects[[1]]$contributors[[34]]$laboratory
## [1] "National Heart and Lung Institute"
## 
## $projects[[1]]$contributors[[34]]$correspondingContributor
## NULL
## 
## $projects[[1]]$contributors[[34]]$email
## [1] "michael.lee@imperial.ac.uk"
## 
## 
## 
## $projects[[1]]$publications
## $projects[[1]]$publications[[1]]
## $projects[[1]]$publications[[1]]$publicationTitle
## [1] "Cells of the adult human heart"
## 
## $projects[[1]]$publications[[1]]$publicationUrl
## [1] "https://www.nature.com/articles/s41586-020-2797-4"
## 
## 
## 
## $projects[[1]]$arrayExpressAccessions
## $projects[[1]]$arrayExpressAccessions[[1]]
## NULL
## 
## 
## $projects[[1]]$geoSeriesAccessions
## $projects[[1]]$geoSeriesAccessions[[1]]
## NULL
## 
## 
## $projects[[1]]$insdcProjectAccessions
## $projects[[1]]$insdcProjectAccessions[[1]]
## [1] "ERP123138"
## 
## 
## $projects[[1]]$insdcStudyAccessions
## $projects[[1]]$insdcStudyAccessions[[1]]
## [1] "PRJEB39602"
## 
## 
## $projects[[1]]$supplementaryLinks
## $projects[[1]]$supplementaryLinks[[1]]
## [1] "https://www.heartcellatlas.org/"
## 
## 
## $projects[[1]]$matrices
## $projects[[1]]$matrices$genusSpecies
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$submissionDate
## [1] "2021-02-11T10:30:00.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$updateDate
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription[[1]]
## [1] "Count Matrix"
## 
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$format
## [1] "loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$isIntermediate
## [1] FALSE
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$name
## [1] "human-heart-10XV3.loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$sha256
## [1] "ee31af654eb2008c8748875b117ee7eecd70ad63ed93811144fb44651144c3ca"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$size
## [1] 3255905369
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$fileSource
## [1] "DCP/2 Analysis"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$uuid
## [1] "b0cd671e-a918-51db-ba29-e127caf325c5"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$version
## [1] "2021-02-13T01:32:57.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$matrixCellCount
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b0cd671e-a918-51db-ba29-e127caf325c5?catalog=dcp10&version=2021-02-13T01%3A32%3A57.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$matrix_cell_count
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$source
## [1] "DCP/2 Analysis"
## 
## 
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' 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]]$submissionDate
## [1] "2021-02-11T18:30:00.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$updateDate
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription[[1]]
## [1] "Count Matrix"
## 
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$format
## [1] "loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$isIntermediate
## [1] FALSE
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$name
## [1] "human-heart-10XV2.loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$sha256
## [1] "d38c4fe7ef2bfb28f42854e447ba65929bbcd89023211c1bff0e34674bede78e"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$size
## [1] 4398007571
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$fileSource
## [1] "DCP/2 Analysis"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "dc58c876-3de2-5264-b108-531d4e6c914a"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-15T14:15:05.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrixCellCount
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/dc58c876-3de2-5264-b108-531d4e6c914a?catalog=dcp10&version=2021-02-15T14%3A15%3A05.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrix_cell_count
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$`human adult stage`$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$source
## [1] "DCP/2 Analysis"
## 
## 
## 
## 
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$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]]$submissionDate
## [1] "2021-02-11T18:30:00.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$updateDate
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription[[1]]
## [1] "Count Matrix"
## 
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$format
## [1] "loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$isIntermediate
## [1] FALSE
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$name
## [1] "human-heart-10XV2.loom"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$sha256
## [1] "d38c4fe7ef2bfb28f42854e447ba65929bbcd89023211c1bff0e34674bede78e"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$size
## [1] 4398007571
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$fileSource
## [1] "DCP/2 Analysis"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$uuid
## [1] "dc58c876-3de2-5264-b108-531d4e6c914a"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$version
## [1] "2021-02-15T14:15:05.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrixCellCount
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/dc58c876-3de2-5264-b108-531d4e6c914a?catalog=dcp10&version=2021-02-15T14%3A15%3A05.000000Z"
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrix_cell_count
## NULL
## 
## $projects[[1]]$matrices$genusSpecies$`Homo sapiens`$organ$heart$developmentStage$adult$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$source
## [1] "DCP/2 Analysis"
## 
## 
## 
## 
## 
## 
## 
## 
## 
## 
## 
## $projects[[1]]$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]]$submissionDate
## [1] "2021-02-10T17:01:03.177554Z"
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$updateDate
## [1] "2021-02-10T17:01:03.177554Z"
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$contentDescription[[1]]
## [1] "Matrix"
## 
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$format
## [1] "h5ad"
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$isIntermediate
## [1] FALSE
## 
## $projects[[1]]$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]]$sha256
## [1] "80917c4e67e581ee2696691ddd4b031bf45cbc7ba77757c8a203cd88c15f9c3f"
## 
## $projects[[1]]$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]]$fileSource
## [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]]$matrixCellCount
## NULL
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b30d1a16-fb04-5ac7-999f-6ce9d1de0c76?catalog=dcp10&version=2021-02-10T17%3A01%3A03.177554Z"
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$matrix_cell_count
## NULL
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10X 3' v2 sequencing`[[1]]$source
## [1] "Contributor"
## 
## 
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' 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]]$submissionDate
## [1] "2021-02-10T17:01:03.177554Z"
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$updateDate
## [1] "2021-02-10T17:01:03.177554Z"
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$contentDescription[[1]]
## [1] "Matrix"
## 
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$format
## [1] "h5ad"
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$isIntermediate
## [1] FALSE
## 
## $projects[[1]]$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]]$sha256
## [1] "80917c4e67e581ee2696691ddd4b031bf45cbc7ba77757c8a203cd88c15f9c3f"
## 
## $projects[[1]]$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]]$fileSource
## [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]]$matrixCellCount
## NULL
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$url
## [1] "https://service.azul.data.humancellatlas.org/repository/files/b30d1a16-fb04-5ac7-999f-6ce9d1de0c76?catalog=dcp10&version=2021-02-10T17%3A01%3A03.177554Z"
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$matrix_cell_count
## NULL
## 
## $projects[[1]]$contributorMatrices$genusSpecies$`Homo sapiens`$developmentStage$adult$organ$heart$libraryConstructionApproach$`10x 3' v3 sequencing`[[1]]$source
## [1] "Contributor"
## 
## 
## 
## 
## 
## 
## 
## 
## 
## 
## 
## $projects[[1]]$accessions
## $projects[[1]]$accessions[[1]]
## $projects[[1]]$accessions[[1]]$namespace
## [1] "biostudies"
## 
## $projects[[1]]$accessions[[1]]$accession
## [1] "S-SUBS13"
## 
## 
## $projects[[1]]$accessions[[2]]
## $projects[[1]]$accessions[[2]]$namespace
## [1] "insdc_project"
## 
## $projects[[1]]$accessions[[2]]$accession
## [1] "ERP123138"
## 
## 
## $projects[[1]]$accessions[[3]]
## $projects[[1]]$accessions[[3]]$namespace
## [1] "insdc_study"
## 
## $projects[[1]]$accessions[[3]]$accession
## [1] "PRJEB39602"
## 
## 
## 
## $projects[[1]]$accessible
## [1] TRUE
## 
## 
## 
## $samples
## $samples[[1]]
## $samples[[1]]$sampleEntityType
## $samples[[1]]$sampleEntityType[[1]]
## [1] "specimens"
## 
## 
## $samples[[1]]$effectiveOrgan
## $samples[[1]]$effectiveOrgan[[1]]
## [1] "heart"
## 
## 
## $samples[[1]]$submissionDate
## [1] "2020-07-24T16:38:59.726000Z"
## 
## $samples[[1]]$updateDate
## [1] "2020-10-22T14:33:34.919000Z"
## 
## $samples[[1]]$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]]
## $specimens[[1]]$submissionDate
## [1] "2020-07-24T16:38:59.726000Z"
## 
## $specimens[[1]]$updateDate
## [1] "2020-10-22T14:33:34.919000Z"
## 
## $specimens[[1]]$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]]
## $donorOrganisms[[1]]$submissionDate
## [1] "2020-07-24T16:38:59.599000Z"
## 
## $donorOrganisms[[1]]$updateDate
## [1] "2020-10-22T14:33:45.449000Z"
## 
## $donorOrganisms[[1]]$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]]
## $cellSuspensions[[1]]$submissionDate
## [1] "2020-07-24T16:39:00.529000Z"
## 
## $cellSuspensions[[1]]$updateDate
## [1] "2020-10-22T14:33:39.577000Z"
## 
## $cellSuspensions[[1]]$organ
## $cellSuspensions[[1]]$organ[[1]]
## [1] "heart"
## 
## 
## $cellSuspensions[[1]]$organPart
## $cellSuspensions[[1]]$organPart[[1]]
## [1] "apex of heart"
## 
## $cellSuspensions[[1]]$organPart[[2]]
## [1] "heart left ventricle"
## 
## $cellSuspensions[[1]]$organPart[[3]]
## [1] "heart right ventricle"
## 
## $cellSuspensions[[1]]$organPart[[4]]
## [1] "interventricular septum"
## 
## $cellSuspensions[[1]]$organPart[[5]]
## [1] "left cardiac atrium"
## 
## $cellSuspensions[[1]]$organPart[[6]]
## [1] "right cardiac atrium"
## 
## 
## $cellSuspensions[[1]]$selectedCellType
## $cellSuspensions[[1]]$selectedCellType[[1]]
## NULL
## 
## 
## $cellSuspensions[[1]]$totalCells
## [1] 791000
## 
## 
## 
## $fileTypeSummaries
## $fileTypeSummaries[[1]]
## $fileTypeSummaries[[1]]$format
## [1] "fastq.gz"
## 
## $fileTypeSummaries[[1]]$fileType
## [1] "fastq.gz"
## 
## $fileTypeSummaries[[1]]$fileSource
## $fileTypeSummaries[[1]]$fileSource[[1]]
## NULL
## 
## 
## $fileTypeSummaries[[1]]$source
## $fileTypeSummaries[[1]]$source[[1]]
## NULL
## 
## 
## $fileTypeSummaries[[1]]$count
## [1] 768
## 
## $fileTypeSummaries[[1]]$totalSize
## [1] 3.05423e+12
## 
## $fileTypeSummaries[[1]]$matrixCellCount
## NULL
## 
## $fileTypeSummaries[[1]]$isIntermediate
## NULL
## 
## $fileTypeSummaries[[1]]$contentDescription
## $fileTypeSummaries[[1]]$contentDescription[[1]]
## [1] "DNA sequence"
## 
## 
## 
## $fileTypeSummaries[[2]]
## $fileTypeSummaries[[2]]$format
## [1] "loom"
## 
## $fileTypeSummaries[[2]]$fileType
## [1] "loom"
## 
## $fileTypeSummaries[[2]]$fileSource
## $fileTypeSummaries[[2]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
## 
## 
## $fileTypeSummaries[[2]]$source
## $fileTypeSummaries[[2]]$source[[1]]
## [1] "DCP/2 Analysis"
## 
## 
## $fileTypeSummaries[[2]]$count
## [1] 148
## 
## $fileTypeSummaries[[2]]$totalSize
## [1] 286860224345
## 
## $fileTypeSummaries[[2]]$matrixCellCount
## NULL
## 
## $fileTypeSummaries[[2]]$isIntermediate
## [1] TRUE
## 
## $fileTypeSummaries[[2]]$contentDescription
## $fileTypeSummaries[[2]]$contentDescription[[1]]
## [1] "Count Matrix"
## 
## 
## 
## $fileTypeSummaries[[3]]
## $fileTypeSummaries[[3]]$format
## [1] "bam"
## 
## $fileTypeSummaries[[3]]$fileType
## [1] "bam"
## 
## $fileTypeSummaries[[3]]$fileSource
## $fileTypeSummaries[[3]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
## 
## 
## $fileTypeSummaries[[3]]$source
## $fileTypeSummaries[[3]]$source[[1]]
## [1] "DCP/2 Analysis"
## 
## 
## $fileTypeSummaries[[3]]$count
## [1] 148
## 
## $fileTypeSummaries[[3]]$totalSize
## [1] 2.703466e+12
## 
## $fileTypeSummaries[[3]]$matrixCellCount
## NULL
## 
## $fileTypeSummaries[[3]]$isIntermediate
## NULL
## 
## $fileTypeSummaries[[3]]$contentDescription
## $fileTypeSummaries[[3]]$contentDescription[[1]]
## NULL
## 
## 
## 
## $fileTypeSummaries[[4]]
## $fileTypeSummaries[[4]]$format
## [1] "h5ad"
## 
## $fileTypeSummaries[[4]]$fileType
## [1] "h5ad"
## 
## $fileTypeSummaries[[4]]$fileSource
## $fileTypeSummaries[[4]]$fileSource[[1]]
## [1] "Contributor"
## 
## 
## $fileTypeSummaries[[4]]$source
## $fileTypeSummaries[[4]]$source[[1]]
## [1] "Contributor"
## 
## 
## $fileTypeSummaries[[4]]$count
## [1] 1
## 
## $fileTypeSummaries[[4]]$totalSize
## [1] 5068859764
## 
## $fileTypeSummaries[[4]]$matrixCellCount
## NULL
## 
## $fileTypeSummaries[[4]]$isIntermediate
## [1] FALSE
## 
## $fileTypeSummaries[[4]]$contentDescription
## $fileTypeSummaries[[4]]$contentDescription[[1]]
## [1] "Matrix"
## 
## 
## 
## $fileTypeSummaries[[5]]
## $fileTypeSummaries[[5]]$format
## [1] "loom"
## 
## $fileTypeSummaries[[5]]$fileType
## [1] "loom"
## 
## $fileTypeSummaries[[5]]$fileSource
## $fileTypeSummaries[[5]]$fileSource[[1]]
## [1] "DCP/2 Analysis"
## 
## 
## $fileTypeSummaries[[5]]$source
## $fileTypeSummaries[[5]]$source[[1]]
## [1] "DCP/2 Analysis"
## 
## 
## $fileTypeSummaries[[5]]$count
## [1] 2
## 
## $fileTypeSummaries[[5]]$totalSize
## [1] 7653912940
## 
## $fileTypeSummaries[[5]]$matrixCellCount
## NULL
## 
## $fileTypeSummaries[[5]]$isIntermediate
## [1] FALSE
## 
## $fileTypeSummaries[[5]]$contentDescription
## $fileTypeSummaries[[5]]$contentDescription[[1]]
## [1] "Count Matrix"

9 Exploring manifest files

See the accompanying “Human Cell Atlas Manifests” vignette on details pertaining to the use of the manifest endpoint and further annotation of .loom files

10 Session info

sessionInfo()
## R Under development (unstable) (2021-10-19 r81077)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] httr_1.4.2                  hca_1.3.0                  
##  [3] LoomExperiment_1.13.0       BiocIO_1.5.0               
##  [5] rhdf5_2.39.0                SingleCellExperiment_1.17.0
##  [7] SummarizedExperiment_1.25.0 Biobase_2.55.0             
##  [9] GenomicRanges_1.47.0        GenomeInfoDb_1.31.0        
## [11] IRanges_2.29.0              S4Vectors_0.33.0           
## [13] BiocGenerics_0.41.0         MatrixGenerics_1.7.0       
## [15] matrixStats_0.61.0          dplyr_1.0.7                
## [17] BiocStyle_2.23.0           
## 
## loaded via a namespace (and not attached):
##  [1] tidyr_1.1.4            sass_0.4.0             vroom_1.5.5           
##  [4] bit64_4.0.5            jsonlite_1.7.2         bslib_0.3.1           
##  [7] assertthat_0.2.1       BiocManager_1.30.16    BiocFileCache_2.3.0   
## [10] blob_1.2.2             GenomeInfoDbData_1.2.7 yaml_2.2.1            
## [13] pillar_1.6.4           RSQLite_2.2.8          lattice_0.20-45       
## [16] glue_1.4.2             digest_0.6.28          XVector_0.35.0        
## [19] htmltools_0.5.2        Matrix_1.3-4           pkgconfig_2.0.3       
## [22] bookdown_0.24          zlibbioc_1.41.0        purrr_0.3.4           
## [25] HDF5Array_1.23.0       tzdb_0.1.2             tibble_3.1.5          
## [28] generics_0.1.1         ellipsis_0.3.2         withr_2.4.2           
## [31] cachem_1.0.6           cli_3.0.1              magrittr_2.0.1        
## [34] crayon_1.4.1           memoise_2.0.0          evaluate_0.14         
## [37] fansi_0.5.0            tools_4.2.0            hms_1.1.1             
## [40] formatR_1.11           lifecycle_1.0.1        stringr_1.4.0         
## [43] Rhdf5lib_1.17.0        DelayedArray_0.21.0    lambda.r_1.2.4        
## [46] compiler_4.2.0         jquerylib_0.1.4        rlang_0.4.12          
## [49] futile.logger_1.4.3    grid_4.2.0             RCurl_1.98-1.5        
## [52] rhdf5filters_1.7.0     rappdirs_0.3.3         bitops_1.0-7          
## [55] rmarkdown_2.11         DBI_1.1.1              curl_4.3.2            
## [58] R6_2.5.1               knitr_1.36             fastmap_1.1.0         
## [61] bit_4.0.4              utf8_1.2.2             filelock_1.0.2        
## [64] futile.options_1.0.1   readr_2.0.2            stringi_1.7.5         
## [67] parallel_4.2.0         Rcpp_1.0.7             vctrs_0.3.8           
## [70] dbplyr_2.1.1           tidyselect_1.1.1       xfun_0.27