Contents

1 Motivation & Introduction

The purpose of this vignette is to explore the file manifests available from the Human Cell Atlas project.

These files provide a metadata summary for a collection of files in a tabular format, including but not limited to information about process and workflow used to generate the file, information about the specimens the file data were derived from, and identifiers connect specific projects, files, and specimens.

The WARP (WDL Analysis Research Pipelines) repository contains information on a variety of pipelines, and can be used alongside a manifest to better understand the metadata.

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("LoomExperiment", "hca")
pkgs_needed <- pkgs[!pkgs %in% rownames(installed.packages())]
BiocManager::install(pkgs_needed)

Load the packages into your R session.

library(dplyr)
library(SummarizedExperiment)
library(LoomExperiment)
library(hca)

2 Example: Default function parameters

default_manifest_tbl <- hca::manifest()
default_manifest_tbl
## # A tibble: 360,690 × 56
##    source_id   source_spec    bundle_uuid  bundle_version      file_document_id 
##    <chr>       <chr>          <chr>        <dttm>              <chr>            
##  1 1cbf0879-2… tdr:tdr-fp-43… ffed96bd-be… 2021-05-14 13:58:58 0000591a-0df3-40…
##  2 1cbf0879-2… tdr:tdr-fp-43… 4ef10b20-d5… 2019-08-01 20:01:47 0000c13f-a299-48…
##  3 1cbf0879-2… tdr:tdr-fp-43… 0d43b1a9-71… 2019-05-17 16:05:38 0001010d-8f9a-41…
##  4 1cbf0879-2… tdr:tdr-fp-43… 2fb448ac-38… 2021-02-25 20:02:24 00014fc3-7451-43…
##  5 1cbf0879-2… tdr:tdr-fp-43… 2a61bc39-23… 2019-08-01 20:01:47 0001614e-b44f-46…
##  6 1cbf0879-2… tdr:tdr-fp-43… 17eb537d-b9… 2019-05-16 21:18:13 00016bff-87d4-47…
##  7 1cbf0879-2… tdr:tdr-fp-43… 894980d6-f3… 2021-06-10 09:50:55 00016dd1-216e-4b…
##  8 1cbf0879-2… tdr:tdr-fp-43… 0678bd67-ff… 2019-08-01 20:01:47 000183e4-19f4-43…
##  9 1cbf0879-2… tdr:tdr-fp-43… aa7364b0-c4… 2021-05-14 13:58:53 000189b0-671a-45…
## 10 1cbf0879-2… tdr:tdr-fp-43… 2d556dfb-0f… 2019-08-01 20:01:46 0001b474-e38d-49…
## # … with 360,680 more rows, and 51 more variables: file_type <chr>,
## #   file_name <chr>, file_format <chr>, read_index <chr>, file_size <dbl>,
## #   file_uuid <chr>, file_version <dttm>, file_crc32c <chr>, file_sha256 <chr>,
## #   file_content_type <chr>, file_drs_uri <chr>, file_url <chr>,
## #   cell_suspension.provenance.document_id <chr>,
## #   cell_suspension.biomaterial_core.biomaterial_id <chr>,
## #   cell_suspension.estimated_cell_count <dbl>, …

3 Example: Manifest for specific criteria

manifest_filter <- hca::filters(
    projectId = list(is = "4a95101c-9ffc-4f30-a809-f04518a23803"),
    fileFormat = list(is = "loom"),
    workflow = list(is = c("optimus_v4.2.2", "optimus_v4.2.3"))
)

manifest_tibble <- hca::manifest(filters = manifest_filter)
manifest_tibble
## # A tibble: 20 × 56
##    source_id   source_spec    bundle_uuid  bundle_version      file_document_id 
##    <chr>       <chr>          <chr>        <dttm>              <chr>            
##  1 1cbf0879-2… tdr:tdr-fp-43… b593b66a-d2… 2020-02-03 01:00:00 131ea511-25f7-58…
##  2 1cbf0879-2… tdr:tdr-fp-43… 5a63dd0b-52… 2021-02-02 23:50:00 1bb375a5-d22b-59…
##  3 1cbf0879-2… tdr:tdr-fp-43… 40733888-3b… 2021-02-02 23:55:00 1f8ff0fa-6892-5e…
##  4 1cbf0879-2… tdr:tdr-fp-43… 1a41ebe6-ee… 2021-02-02 23:50:00 2fffe225-ba6c-59…
##  5 1cbf0879-2… tdr:tdr-fp-43… c12a6ca2-32… 2021-02-02 23:50:00 31aa5a18-2a4e-54…
##  6 1cbf0879-2… tdr:tdr-fp-43… f58d690c-bb… 2021-02-02 23:50:00 48eea299-8823-5a…
##  7 1cbf0879-2… tdr:tdr-fp-43… 21c4e2de-ec… 2021-02-02 23:50:00 51458973-404c-58…
##  8 1cbf0879-2… tdr:tdr-fp-43… 50620c50-23… 2021-02-02 23:50:00 5bbebef4-9b14-50…
##  9 1cbf0879-2… tdr:tdr-fp-43… e3ecdfc2-44… 2021-02-02 23:55:00 5bc232f2-b77c-52…
## 10 1cbf0879-2… tdr:tdr-fp-43… ae338c4e-65… 2021-02-02 23:50:00 6326b602-0f63-54…
## 11 1cbf0879-2… tdr:tdr-fp-43… d62c4599-47… 2020-02-03 01:00:00 7848d80b-6b1d-56…
## 12 1cbf0879-2… tdr:tdr-fp-43… 81df106e-e7… 2021-02-02 23:55:00 9f8bc032-6276-57…
## 13 1cbf0879-2… tdr:tdr-fp-43… 2838323c-cd… 2020-02-03 01:00:00 b98cfaac-64f5-59…
## 14 1cbf0879-2… tdr:tdr-fp-43… c3f672ad-e6… 2021-02-02 23:50:00 bf7751ae-ac9d-5b…
## 15 1cbf0879-2… tdr:tdr-fp-43… a9c90392-ca… 2020-02-03 01:00:00 c7b6470c-e2f0-51…
## 16 1cbf0879-2… tdr:tdr-fp-43… 9d0f5cd1-0e… 2020-02-03 01:00:00 d0b95f2c-98ae-58…
## 17 1cbf0879-2… tdr:tdr-fp-43… 59de15e1-f5… 2021-02-02 23:50:00 d18759a6-2a95-5d…
## 18 1cbf0879-2… tdr:tdr-fp-43… 54fb0e25-57… 2021-02-02 23:55:00 dfd9905b-d6c9-5a…
## 19 1cbf0879-2… tdr:tdr-fp-43… 7516565a-e8… 2021-02-02 23:55:00 e07ca731-b20a-5b…
## 20 1cbf0879-2… tdr:tdr-fp-43… 8e850d2d-0b… 2021-02-02 23:50:00 fd41f3d6-7664-53…
## # … with 51 more variables: file_type <chr>, file_name <chr>,
## #   file_format <chr>, read_index <lgl>, file_size <dbl>, file_uuid <chr>,
## #   file_version <dttm>, file_crc32c <chr>, file_sha256 <chr>,
## #   file_content_type <chr>, file_drs_uri <chr>, file_url <chr>,
## #   cell_suspension.provenance.document_id <chr>,
## #   cell_suspension.biomaterial_core.biomaterial_id <chr>,
## #   cell_suspension.estimated_cell_count <lgl>, …

## what specimen organs are represented in these files?
manifest_tibble |>
    dplyr::count(specimen_from_organism.organ)
## # A tibble: 4 × 2
##   specimen_from_organism.organ     n
##   <chr>                        <int>
## 1 blood                            5
## 2 hematopoietic system             5
## 3 lung                             5
## 4 mediastinal lymph node           5

4 Example: Using manifest data to select files

manifest_tibble
## # A tibble: 20 × 56
##    source_id   source_spec    bundle_uuid  bundle_version      file_document_id 
##    <chr>       <chr>          <chr>        <dttm>              <chr>            
##  1 1cbf0879-2… tdr:tdr-fp-43… b593b66a-d2… 2020-02-03 01:00:00 131ea511-25f7-58…
##  2 1cbf0879-2… tdr:tdr-fp-43… 5a63dd0b-52… 2021-02-02 23:50:00 1bb375a5-d22b-59…
##  3 1cbf0879-2… tdr:tdr-fp-43… 40733888-3b… 2021-02-02 23:55:00 1f8ff0fa-6892-5e…
##  4 1cbf0879-2… tdr:tdr-fp-43… 1a41ebe6-ee… 2021-02-02 23:50:00 2fffe225-ba6c-59…
##  5 1cbf0879-2… tdr:tdr-fp-43… c12a6ca2-32… 2021-02-02 23:50:00 31aa5a18-2a4e-54…
##  6 1cbf0879-2… tdr:tdr-fp-43… f58d690c-bb… 2021-02-02 23:50:00 48eea299-8823-5a…
##  7 1cbf0879-2… tdr:tdr-fp-43… 21c4e2de-ec… 2021-02-02 23:50:00 51458973-404c-58…
##  8 1cbf0879-2… tdr:tdr-fp-43… 50620c50-23… 2021-02-02 23:50:00 5bbebef4-9b14-50…
##  9 1cbf0879-2… tdr:tdr-fp-43… e3ecdfc2-44… 2021-02-02 23:55:00 5bc232f2-b77c-52…
## 10 1cbf0879-2… tdr:tdr-fp-43… ae338c4e-65… 2021-02-02 23:50:00 6326b602-0f63-54…
## 11 1cbf0879-2… tdr:tdr-fp-43… d62c4599-47… 2020-02-03 01:00:00 7848d80b-6b1d-56…
## 12 1cbf0879-2… tdr:tdr-fp-43… 81df106e-e7… 2021-02-02 23:55:00 9f8bc032-6276-57…
## 13 1cbf0879-2… tdr:tdr-fp-43… 2838323c-cd… 2020-02-03 01:00:00 b98cfaac-64f5-59…
## 14 1cbf0879-2… tdr:tdr-fp-43… c3f672ad-e6… 2021-02-02 23:50:00 bf7751ae-ac9d-5b…
## 15 1cbf0879-2… tdr:tdr-fp-43… a9c90392-ca… 2020-02-03 01:00:00 c7b6470c-e2f0-51…
## 16 1cbf0879-2… tdr:tdr-fp-43… 9d0f5cd1-0e… 2020-02-03 01:00:00 d0b95f2c-98ae-58…
## 17 1cbf0879-2… tdr:tdr-fp-43… 59de15e1-f5… 2021-02-02 23:50:00 d18759a6-2a95-5d…
## 18 1cbf0879-2… tdr:tdr-fp-43… 54fb0e25-57… 2021-02-02 23:55:00 dfd9905b-d6c9-5a…
## 19 1cbf0879-2… tdr:tdr-fp-43… 7516565a-e8… 2021-02-02 23:55:00 e07ca731-b20a-5b…
## 20 1cbf0879-2… tdr:tdr-fp-43… 8e850d2d-0b… 2021-02-02 23:50:00 fd41f3d6-7664-53…
## # … with 51 more variables: file_type <chr>, file_name <chr>,
## #   file_format <chr>, read_index <lgl>, file_size <dbl>, file_uuid <chr>,
## #   file_version <dttm>, file_crc32c <chr>, file_sha256 <chr>,
## #   file_content_type <chr>, file_drs_uri <chr>, file_url <chr>,
## #   cell_suspension.provenance.document_id <chr>,
## #   cell_suspension.biomaterial_core.biomaterial_id <chr>,
## #   cell_suspension.estimated_cell_count <lgl>, …
file_uuid <- "24a8a323-7ecd-504e-a253-b0e0892dd730"
file_filter <- hca::filters(
    fileId = list(is = file_uuid)
)

file_tbl <- hca::files(filters = file_filter)

file_tbl
## # A tibble: 1 × 8
##   fileId   name    fileFormat    size version projectTitle   projectId  url     
##   <chr>    <chr>   <chr>        <int> <chr>   <chr>          <chr>      <chr>   
## 1 24a8a32… t-cell… loom        3.90e8 2021-0… A single-cell… 4a95101c-… https:/…
file_location <-
    file_tbl |>
    hca::files_download()
file_location
## 24a8a323-7ecd-504e-a253-b0e0892dd730-2021-02-11T19:00:05.000000Z 
##  "/home/biocbuild/.cache/R/hca/67e0625998803_67e0625998803.loom"
loom <- LoomExperiment::import(file_location)
metadata(loom) |>
    dplyr::glimpse()
## List of 15
##  $ last_modified                                             : chr "20210211T185949.186062Z"
##  $ CreationDate                                              : chr "20210211T185658.758915Z"
##  $ LOOM_SPEC_VERSION                                         : chr "3.0.0"
##  $ donor_organism.genus_species                              : chr "Homo sapiens"
##  $ expression_data_type                                      : chr "exonic"
##  $ input_id                                                  : chr "58a18a4c-5423-4c59-9b3c-50b7f30b1ca5, c763f679-e13d-4f81-844f-c2c80fc90f46, c76d90b8-c190-4c58-b9bc-b31f586ec7f"| __truncated__
##  $ input_id_metadata_field                                   : chr "sequencing_process.provenance.document_id"
##  $ input_name                                                : chr "PP012_suspension, PP003_suspension, PP004_suspension, PP011_suspension"
##  $ input_name_metadata_field                                 : chr "sequencing_input.biomaterial_core.biomaterial_id"
##  $ library_preparation_protocol.library_construction_approach: chr "10X v2 sequencing"
##  $ optimus_output_schema_version                             : chr "1.0.0"
##  $ pipeline_version                                          : chr "Optimus_v4.2.2"
##  $ project.project_core.project_name                         : chr "HumanTissueTcellActivation"
##  $ project.provenance.document_id                            : chr "4a95101c-9ffc-4f30-a809-f04518a23803"
##  $ specimen_from_organism.organ                              : chr "hematopoietic system"
colData(loom) |>
    dplyr::as_tibble() |>
    dplyr::glimpse()
## Rows: 91,713
## Columns: 43
## $ CellID                                                 <chr> "GCTTCCATCACCGT…
## $ antisense_reads                                        <int> 0, 0, 0, 0, 0, …
## $ cell_barcode_fraction_bases_above_30_mean              <dbl> 0.9846281, 0.98…
## $ cell_barcode_fraction_bases_above_30_variance          <dbl> 0.003249023, 0.…
## $ cell_names                                             <chr> "GCTTCCATCACCGT…
## $ duplicate_reads                                        <int> 0, 0, 0, 0, 0, …
## $ emptydrops_FDR                                         <dbl> 1.000000000, 0.…
## $ emptydrops_IsCell                                      <raw> 00, 01, 00, 00,…
## $ emptydrops_Limited                                     <raw> 00, 01, 00, 00,…
## $ emptydrops_LogProb                                     <dbl> -689.6831, -120…
## $ emptydrops_PValue                                      <dbl> 0.91840816, 0.0…
## $ emptydrops_Total                                       <int> 255, 16705, 681…
## $ fragments_per_molecule                                 <dbl> 1.693252, 8.453…
## $ fragments_with_single_read_evidence                    <int> 504, 139828, 58…
## $ genes_detected_multiple_observations                   <int> 82, 2873, 1552,…
## $ genomic_read_quality_mean                              <dbl> 36.62988, 36.87…
## $ genomic_read_quality_variance                          <dbl> 25.99015, 20.19…
## $ genomic_reads_fraction_bases_quality_above_30_mean     <dbl> 0.8584288, 0.86…
## $ genomic_reads_fraction_bases_quality_above_30_variance <dbl> 0.03981779, 0.0…
## $ input_id                                               <chr> "58a18a4c-5423-…
## $ molecule_barcode_fraction_bases_above_30_mean          <dbl> 0.9820324, 0.98…
## $ molecule_barcode_fraction_bases_above_30_variance      <dbl> 0.005782884, 0.…
## $ molecules_with_single_read_evidence                    <int> 276, 5028, 2041…
## $ n_fragments                                            <int> 552, 202060, 84…
## $ n_genes                                                <int> 227, 3381, 1826…
## $ n_mitochondrial_genes                                  <int> 5, 22, 17, 5, 2…
## $ n_mitochondrial_molecules                              <int> 8, 3528, 2928, …
## $ n_molecules                                            <int> 326, 23902, 998…
## $ n_reads                                                <int> 679, 341669, 13…
## $ noise_reads                                            <int> 0, 0, 0, 0, 0, …
## $ pct_mitochondrial_molecules                            <dbl> 1.1782032, 1.03…
## $ perfect_cell_barcodes                                  <int> 667, 336674, 13…
## $ perfect_molecule_barcodes                              <int> 384, 227854, 89…
## $ reads_mapped_exonic                                    <int> 343, 210716, 84…
## $ reads_mapped_intergenic                                <int> 39, 19439, 8042…
## $ reads_mapped_intronic                                  <int> 175, 58833, 276…
## $ reads_mapped_multiple                                  <int> 162, 90968, 365…
## $ reads_mapped_too_many_loci                             <int> 0, 0, 0, 0, 0, …
## $ reads_mapped_uniquely                                  <int> 450, 227309, 93…
## $ reads_mapped_utr                                       <int> 55, 29289, 1039…
## $ reads_per_fragment                                     <dbl> 1.230072, 1.690…
## $ reads_unmapped                                         <int> 67, 23392, 9340…
## $ spliced_reads                                          <int> 99, 73817, 2987…

5 Example: Using manifest data to annotate a .loom file

The function optimus_loom_annotation() takes in the file path of a .loom file generated by the Optimus pipeline and returns a LoomExperiment object whose colData has been annotated with additional specimen data extracted from a manifest.

annotated_loom <- optimus_loom_annotation(file_location)
annotated_loom
## class: SingleCellLoomExperiment 
## dim: 58347 91713 
## metadata(16): last_modified CreationDate ...
##   specimen_from_organism.organ manifest
## assays(1): matrix
## rownames: NULL
## rowData names(29): Gene antisense_reads ... reads_per_molecule
##   spliced_reads
## colnames: NULL
## colData names(98): input_id CellID ...
##   sequencing_input.biomaterial_core.biomaterial_id
##   sequencing_input_type
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowGraphs(0): NULL
## colGraphs(0): NULL


## new metadata
setdiff(
    names(metadata(annotated_loom)),
    names(metadata(loom))
)
## [1] "manifest"
metadata(annotated_loom)$manifest
## # A tibble: 4 × 56
##   source_id   source_spec     bundle_uuid  bundle_version      file_document_id 
##   <chr>       <chr>           <chr>        <dttm>              <chr>            
## 1 1cbf0879-2… tdr:tdr-fp-431… e3ecdfc2-44… 2021-02-02 23:55:00 5bc232f2-b77c-52…
## 2 1cbf0879-2… tdr:tdr-fp-431… 81df106e-e7… 2021-02-02 23:55:00 9f8bc032-6276-57…
## 3 1cbf0879-2… tdr:tdr-fp-431… 54fb0e25-57… 2021-02-02 23:55:00 dfd9905b-d6c9-5a…
## 4 1cbf0879-2… tdr:tdr-fp-431… 7516565a-e8… 2021-02-02 23:55:00 e07ca731-b20a-5b…
## # … with 51 more variables: file_type <chr>, file_name <chr>,
## #   file_format <chr>, read_index <chr>, file_size <dbl>, file_uuid <chr>,
## #   file_version <dttm>, file_crc32c <chr>, file_sha256 <chr>,
## #   file_content_type <chr>, file_drs_uri <chr>, file_url <chr>,
## #   cell_suspension.provenance.document_id <chr>,
## #   cell_suspension.biomaterial_core.biomaterial_id <chr>,
## #   cell_suspension.estimated_cell_count <lgl>, …

## new colData columns
setdiff(
    names(colData(annotated_loom)),
    names(colData(loom))
)
##  [1] "source_id"                                                      
##  [2] "source_spec"                                                    
##  [3] "bundle_uuid"                                                    
##  [4] "bundle_version"                                                 
##  [5] "file_document_id"                                               
##  [6] "file_type"                                                      
##  [7] "file_name"                                                      
##  [8] "file_format"                                                    
##  [9] "read_index"                                                     
## [10] "file_size"                                                      
## [11] "file_uuid"                                                      
## [12] "file_version"                                                   
## [13] "file_crc32c"                                                    
## [14] "file_sha256"                                                    
## [15] "file_content_type"                                              
## [16] "file_drs_uri"                                                   
## [17] "file_url"                                                       
## [18] "cell_suspension.provenance.document_id"                         
## [19] "cell_suspension.biomaterial_core.biomaterial_id"                
## [20] "cell_suspension.estimated_cell_count"                           
## [21] "cell_suspension.selected_cell_type"                             
## [22] "sequencing_protocol.instrument_manufacturer_model"              
## [23] "sequencing_protocol.paired_end"                                 
## [24] "library_preparation_protocol.library_construction_approach"     
## [25] "library_preparation_protocol.nucleic_acid_source"               
## [26] "project.provenance.document_id"                                 
## [27] "project.contributors.institution"                               
## [28] "project.contributors.laboratory"                                
## [29] "project.project_core.project_short_name"                        
## [30] "project.project_core.project_title"                             
## [31] "project.estimated_cell_count"                                   
## [32] "specimen_from_organism.provenance.document_id"                  
## [33] "specimen_from_organism.diseases"                                
## [34] "specimen_from_organism.organ"                                   
## [35] "specimen_from_organism.organ_part"                              
## [36] "specimen_from_organism.preservation_storage.preservation_method"
## [37] "donor_organism.sex"                                             
## [38] "donor_organism.biomaterial_core.biomaterial_id"                 
## [39] "donor_organism.provenance.document_id"                          
## [40] "donor_organism.genus_species"                                   
## [41] "donor_organism.development_stage"                               
## [42] "donor_organism.diseases"                                        
## [43] "donor_organism.organism_age"                                    
## [44] "cell_line.provenance.document_id"                               
## [45] "cell_line.biomaterial_core.biomaterial_id"                      
## [46] "organoid.provenance.document_id"                                
## [47] "organoid.biomaterial_core.biomaterial_id"                       
## [48] "organoid.model_organ"                                           
## [49] "organoid.model_organ_part"                                      
## [50] "_entity_type"                                                   
## [51] "sample.provenance.document_id"                                  
## [52] "sample.biomaterial_core.biomaterial_id"                         
## [53] "sequencing_input.provenance.document_id"                        
## [54] "sequencing_input.biomaterial_core.biomaterial_id"               
## [55] "sequencing_input_type"

6 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] hca_1.3.0                   LoomExperiment_1.13.0      
##  [3] BiocIO_1.5.0                rhdf5_2.39.0               
##  [5] SingleCellExperiment_1.17.0 SummarizedExperiment_1.25.0
##  [7] Biobase_2.55.0              GenomicRanges_1.47.0       
##  [9] GenomeInfoDb_1.31.0         IRanges_2.29.0             
## [11] S4Vectors_0.33.0            BiocGenerics_0.41.0        
## [13] MatrixGenerics_1.7.0        matrixStats_0.61.0         
## [15] dplyr_1.0.7                 BiocStyle_2.23.0           
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.4.2             tidyr_1.1.4            sass_0.4.0            
##  [4] vroom_1.5.5            bit64_4.0.5            jsonlite_1.7.2        
##  [7] bslib_0.3.1            assertthat_0.2.1       BiocManager_1.30.16   
## [10] BiocFileCache_2.3.0    blob_1.2.2             GenomeInfoDbData_1.2.7
## [13] yaml_2.2.1             pillar_1.6.4           RSQLite_2.2.8         
## [16] lattice_0.20-45        glue_1.4.2             digest_0.6.28         
## [19] XVector_0.35.0         htmltools_0.5.2        Matrix_1.3-4          
## [22] pkgconfig_2.0.3        bookdown_0.24          zlibbioc_1.41.0       
## [25] purrr_0.3.4            HDF5Array_1.23.0       tzdb_0.1.2            
## [28] tibble_3.1.5           generics_0.1.1         ellipsis_0.3.2        
## [31] withr_2.4.2            cachem_1.0.6           cli_3.0.1             
## [34] magrittr_2.0.1         crayon_1.4.1           memoise_2.0.0         
## [37] evaluate_0.14          fansi_0.5.0            tools_4.2.0           
## [40] hms_1.1.1              formatR_1.11           lifecycle_1.0.1       
## [43] stringr_1.4.0          Rhdf5lib_1.17.0        DelayedArray_0.21.0   
## [46] lambda.r_1.2.4         compiler_4.2.0         jquerylib_0.1.4       
## [49] rlang_0.4.12           futile.logger_1.4.3    grid_4.2.0            
## [52] RCurl_1.98-1.5         rhdf5filters_1.7.0     rappdirs_0.3.3        
## [55] bitops_1.0-7           rmarkdown_2.11         DBI_1.1.1             
## [58] curl_4.3.2             R6_2.5.1               knitr_1.36            
## [61] fastmap_1.1.0          bit_4.0.4              utf8_1.2.2            
## [64] filelock_1.0.2         futile.options_1.0.1   readr_2.0.2           
## [67] stringi_1.7.5          parallel_4.2.0         Rcpp_1.0.7            
## [70] vctrs_0.3.8            dbplyr_2.1.1           tidyselect_1.1.1      
## [73] xfun_0.27