Rega 0.99.1
library(Rega)Download the empty MS Excel template from
inst/extdata/ega_full_template_v2.xlsx and fill it in according to the
instructions in the ‘Instructions’ tab.
httr2 is built around the notion that the key should live in an environment
variable. So the first step is to make your package key available on your local
development machine by adding a line to your your user-level .Renviron
(which you can easily open with usethis::edit_r_environ())
The REGA_EGA_PASSWORD environmental variable isn’t supposed to store the
password in the plain text, instead:
httr2::secret_make_key() and store it as the
“REGA_KEY” environmental variable (e.g. using export command in bash or
in .Renviron file)httr2::secret_encrypt("<your-ega-password>", "REGA_KEY")Sys.setenv("REGA_EGA_USERNAME" = "<your-ega-username>")
Sys.setenv("REGA_EGA_PASSWORD" = "<your-ega-password>")The default parser parses the bundled xlsx template
(inst/extdata/ega_full_template_v2.xlsx). Changing the parser
behavior, such as whether to append c4gh extension to files or which sheets
to parse from the metadata files is controlled by YAML config file
inst/extdata/default_parser_params.yaml. To modify the parameters,
create a local copy of the file and pass it as param_file argument to
default_parser function.
metadata_file <- system.file(
"extdata/submission_example.xlsx",
package = "Rega"
)
parsed_metadata <- default_parser(metadata_file)
parsed_metadata$aliases
$aliases$studies
[1] "Study1"
$aliases$experiments
[1] "Experiment1"
$aliases$datasets
[1] "Dataset1"
$aliases$samples
[1] "Sample1"
$aliases$runs
[1] "Run1"
$aliases$analyses
[1] "Analysis1"
$files
# A tibble: 1 × 2
file ega_file
<chr> <chr>
1 example.fastq.gz /example.fastq.gz.c4gh
$submission
# A tibble: 1 × 1
title
<chr>
1 Your submission name
$studies
# A tibble: 1 × 4
study title description study_type
<chr> <chr> <chr> <chr>
1 Study1 Example Study Example Study Description Transcriptome Analysis
$samples
# A tibble: 1 × 4
alias phenotype biological_sex subject_id
<chr> <chr> <chr> <chr>
1 Sample1 Control male S1
$experiments
# A tibble: 1 × 8
study experiment design_description library_selection instrument_model_id
<chr> <chr> <chr> <chr> <int>
1 Study1 Experiment1 Expermient Design RANDOM 1
# ℹ 3 more variables: library_layout <chr>, library_strategy <chr>,
# library_source <chr>
$runs
# A tibble: 1 × 5
run experiment run_file_type alias files
<chr> <chr> <chr> <chr> <list>
1 Run1 Experiment1 fastq Sample1 <chr [1]>
$datasets
# A tibble: 1 × 6
dataset title description policy_accession_id dataset_types runs
<chr> <chr> <chr> <chr> <list> <lis>
1 Dataset1 Dataset Title Dataset Descri… EGAP00000000001 <chr [1]> <chr>
$collaborators
# A tibble: 0 × 0
$repositories
# A tibble: 0 × 0
$extra_attributes
# A tibble: 0 × 0
$select_input_data
$select_input_data$study_types
[1] "Whole Genome Sequencing" "Metagenomics"
[3] "Transcriptome Analysis" "Resequencing"
[5] "Epigenetics" "Synthetic Genomics"
[7] "Forensic or Paleo-genomics" "Gene Regulation Study"
[9] "Cancer Genomics" "Population Genomics"
[11] "RNASeq" "Exome Sequencing"
[13] "Pooled Clone Sequencing" "Transcriptome Sequencing"
$select_input_data$biological_sex
[1] "female" "male" "hermaphrodite" "unknown"
$select_input_data$case_controls
[1] "case" "control" "both" "NA"
$select_input_data$platform_models
[1] "1--LS454--454 GS"
[2] "2--LS454--454 GS 20"
[3] "3--LS454--454 GS FLX"
[4] "4--LS454--454 GS FLX+"
[5] "5--LS454--454 GS FLX Titanium"
[6] "6--LS454--454 GS Junior"
[7] "7--LS454--unspecified"
[8] "8--ILLUMINA--HiSeq X Five"
[9] "9--ILLUMINA--HiSeq X Ten"
[10] "10--ILLUMINA--Illumina Genome Analyzer"
[11] "11--ILLUMINA--Illumina Genome Analyzer II"
[12] "12--ILLUMINA--Illumina Genome Analyzer IIx"
[13] "13--ILLUMINA--Illumina HiScanSQ"
[14] "14--ILLUMINA--Illumina HiSeq 1000"
[15] "15--ILLUMINA--Illumina HiSeq 1500"
[16] "16--ILLUMINA--Illumina HiSeq 2000"
[17] "17--ILLUMINA--Illumina HiSeq 2500"
[18] "18--ILLUMINA--Illumina HiSeq 3000"
[19] "19--ILLUMINA--Illumina HiSeq 4000"
[20] "20--ILLUMINA--Illumina HiSeq X"
[21] "21--ILLUMINA--Illumina iSeq 100"
[22] "22--ILLUMINA--Illumina MiSeq"
[23] "23--ILLUMINA--Illumina MiniSeq"
[24] "24--ILLUMINA--Illumina NovaSeq X"
[25] "25--ILLUMINA--Illumina NovaSeq 6000"
[26] "26--ILLUMINA--NextSeq 500"
[27] "27--ILLUMINA--NextSeq 550"
[28] "28--ILLUMINA--NextSeq 1000"
[29] "29--ILLUMINA--NextSeq 2000"
[30] "30--ILLUMINA--unspecified"
[31] "31--HELICOS--Helicos HeliScope"
[32] "32--HELICOS--unspecified"
[33] "33--ABI_SOLID--AB SOLiD System"
[34] "34--ABI_SOLID--AB SOLiD System 2.0"
[35] "35--ABI_SOLID--AB SOLiD System 3.0"
[36] "36--ABI_SOLID--AB SOLiD 3 Plus System"
[37] "37--ABI_SOLID--AB SOLiD 4 System"
[38] "38--ABI_SOLID--AB SOLiD 4hq System"
[39] "39--ABI_SOLID--AB SOLiD PI System"
[40] "40--ABI_SOLID--AB 5500 Genetic Analyzer"
[41] "41--ABI_SOLID--AB 5500xl Genetic Analyzer"
[42] "42--ABI_SOLID--AB 5500xl-W Genetic Analysis System"
[43] "43--ABI_SOLID--unspecified"
[44] "44--COMPLETE_GENOMICS--Complete Genomics"
[45] "45--COMPLETE_GENOMICS--unspecified"
[46] "46--BGISEQ--BGISEQ-50"
[47] "47--BGISEQ--BGISEQ-500"
[48] "48--BGISEQ--MGISEQ-2000RS"
[49] "49--OXFORD_NANOPORE--MinION"
[50] "50--OXFORD_NANOPORE--GridION"
[51] "51--OXFORD_NANOPORE--PromethION"
[52] "52--OXFORD_NANOPORE--unspecified"
[53] "53--PACBIO_SMRT--PacBio RS"
[54] "54--PACBIO_SMRT--PacBio RS II"
[55] "55--PACBIO_SMRT--Sequel"
[56] "56--PACBIO_SMRT--Sequel II"
[57] "57--PACBIO_SMRT--Sequel IIe"
[58] "58--PACBIO_SMRT--unspecified"
[59] "59--ION_TORRENT--Ion Torrent PGM"
[60] "60--ION_TORRENT--Ion Torrent Proton"
[61] "61--ION_TORRENT--Ion Torrent S5"
[62] "62--ION_TORRENT--Ion Torrent S5 XL"
[63] "63--ION_TORRENT--Ion Torrent Genexus"
[64] "64--ION_TORRENT--Ion GeneStudio S5"
[65] "65--ION_TORRENT--Ion GeneStudio S5 Prime"
[66] "66--ION_TORRENT--Ion GeneStudio S5 Plus"
[67] "67--ION_TORRENT--unspecified"
[68] "68--CAPILLARY--AB 3730xL Genetic Analyzer"
[69] "69--CAPILLARY--AB 3730 Genetic Analyzer"
[70] "70--CAPILLARY--AB 3500xL Genetic Analyzer"
[71] "71--CAPILLARY--AB 3500 Genetic Analyzer"
[72] "72--CAPILLARY--AB 3130xL Genetic Analyzer"
[73] "73--CAPILLARY--AB 3130 Genetic Analyzer"
[74] "74--CAPILLARY--AB 310 Genetic Analyzer"
[75] "75--CAPILLARY--unspecified"
[76] "76--DNBSEQ--DNBSEQ-T7"
[77] "77--DNBSEQ--DNBSEQ-G400"
[78] "78--DNBSEQ--DNBSEQ-G50"
[79] "79--DNBSEQ--DNBSEQ-G400 FAST"
[80] "80--DNBSEQ--unspecified"
$select_input_data$library_layouts
[1] "SINGLE" "PAIRED"
$select_input_data$library_strategies
[1] "WGS"
[2] "WGA"
[3] "WXS"
[4] "RNA-Seq"
[5] "ssRNA-seq"
[6] "miRNA-Seq"
[7] "ncRNA-Seq"
[8] "FL-cDNA"
[9] "EST"
[10] "Hi-C"
[11] "ATAC-seq"
[12] "WCS"
[13] "RAD-Seq"
[14] "CLONE"
[15] "POOLCLONE"
[16] "AMPLICON"
[17] "CLONEEND"
[18] "FINISHING"
[19] "ChIP-Seq"
[20] "MNase-Seq"
[21] "DNase-Hypersensitivity"
[22] "Bisulfite-Seq"
[23] "CTS"
[24] "MRE-Seq"
[25] "MeDIP-Seq"
[26] "MBD-Seq"
[27] "Tn-Seq"
[28] "VALIDATION"
[29] "FAIRE-seq"
[30] "SELEX"
[31] "RIP-Seq"
[32] "ChIA-PET"
[33] "Synthetic-Long-Read"
[34] "Targeted-Capture"
[35] "Tethered Chromatin Conformation Capture"
[36] "NOMe-Seq"
[37] "ChM-Seq"
[38] "GBS"
[39] "OTHER"
[40] "snRNA-seq"
[41] "Ribo-Seq"
$select_input_data$library_sources
[1] "GENOMIC" "GENOMIC SINGLE CELL"
[3] "TRANSCRIPTOMIC" "TRANSCRIPTOMIC SINGLE CELL"
[5] "METAGENOMIC" "METATRANSCRIPTOMIC"
[7] "SYNTHETIC" "VIRAL RNA"
[9] "OTHER"
$select_input_data$library_selections
[1] "RANDOM"
[2] "PCR"
[3] "RANDOM PCR"
[4] "RT-PCR"
[5] "HMPR"
[6] "MF"
[7] "repeat fractionation"
[8] "size fractionation"
[9] "MSLL"
[10] "cDNA"
[11] "cDNA_randomPriming"
[12] "cDNA_oligo_dT"
[13] "PolyA"
[14] "Oligo-dT"
[15] "Inverse rRNA"
[16] "Inverse rRNA selection"
[17] "ChIP"
[18] "ChIP-Seq"
[19] "MNase"
[20] "DNase"
[21] "Hybrid Selection"
[22] "Reduced Representation"
[23] "Restriction Digest"
[24] "5-methylcytidine antibody"
[25] "MBD2 protein methyl-CpG binding domain"
[26] "CAGE"
[27] "RACE"
[28] "MDA"
[29] "padlock probes capture method"
[30] "other"
[31] "unspecified"
$select_input_data$run_file_types
[1] "srf--SRF"
[2] "sff--SFF"
[3] "fastq--One/Two Fastq"
[4] "Illumina_native--Illumina"
[5] "Illumina_native_qseq--Illumina QSEQ"
[6] "SOLiD_native_csfasta--SOLiD CSFASTA"
[7] "PacBio_HDF5--PacBio HDF5"
[8] "bam--BAM"
[9] "cram--CRAM"
[10] "CompleteGenomics_native--Complete Genomics"
[11] "OxfordNanopore_native--Oxford Nanopore"
$select_input_data$analysis_types
[1] "REFERENCE ALIGNMENT" "SEQUENCE VARIATION" "SAMPLE PHENOTYPE"
$select_input_data$experiment_types
[1] "Whole genome sequencing" "Whole transcriptome sequencing"
[3] "Exome sequencing" "Genotyping by array"
[5] "transcriptomics" "Curation"
[7] "Genotyping by sequencing" "Target sequencing"
$select_input_data$genomes
[1] "1--29--NCBI36--GCF_000001405.12" "2--1--GRCh37--GCA_000001405.1"
[3] "2--2--GRCh37.p1--GCA_000001405.2" "2--3--GRCh37.p2--GCA_000001405.3"
[5] "2--4--GRCh37.p3--GCA_000001405.4" "2--5--GRCh37.p4--GCA_000001405.5"
[7] "2--6--GRCh37.p5--GCA_000001405.6" "2--7--GRCh37.p6--GCA_000001405.7"
[9] "2--8--GRCh37.p7--GCA_000001405.8" "2--9--GRCh37.p8--GCA_000001405.9"
[11] "2--10--GRCh37.p9--GCA_000001405.10" "2--11--GRCh37.p10--GCA_000001405.11"
[13] "2--12--GRCh37.p11--GCA_000001405.12" "2--13--GRCh37.p12--GCA_000001405.13"
[15] "2--14--GRCh37.p13--GCA_000001405.14" "3--15--GRCh38--GCA_000001405.15"
[17] "3--16--GRCh38.p2--GCA_000001405.17" "3--17--GRCh38.p3--GCA_000001405.18"
[19] "3--18--GRCh38.p4--GCA_000001405.19" "3--19--GRCh38.p5--GCA_000001405.20"
[21] "3--20--GRCh38.p6--GCA_000001405.21" "3--21--GRCh38.p7--GCA_000001405.22"
[23] "3--22--GRCh38.p8--GCA_000001405.23" "3--23--GRCh38.p9--GCA_000001405.24"
[25] "3--24--GRCh38.p10--GCA_000001405.25" "3--25--GRCh38.p11--GCA_000001405.26"
[27] "3--26--GRCh38.p12--GCA_000001405.27" "3--27--GRCh38.p13--GCA_000001405.28"
[29] "3--28--GRCh38.p14--GCA_000001405.29"
$select_input_data$chromosomes
[1] "1--1--chr1--NC_000001.9" "1--2--chr2--NC_000002.10"
[3] "1--3--chr3--NC_000003.10" "1--4--chr4--NC_000004.10"
[5] "1--5--chr5--NC_000005.8" "1--6--chr6--NC_000006.10"
[7] "1--7--chr7--NC_000007.12" "1--8--chr8--NC_000008.9"
[9] "1--9--chr9--NC_000009.10" "1--10--chr10--NC_000010.9"
[11] "1--11--chr11--NC_000011.8" "1--12--chr12--NC_000012.10"
[13] "1--13--chr13--NC_000013.9" "1--14--chr14--NC_000014.7"
[15] "1--15--chr15--NC_000015.8" "1--16--chr16--NC_000016.8"
[17] "1--17--chr17--NC_000017.9" "1--18--chr18--NC_000018.8"
[19] "1--19--chr19--NC_000019.8" "1--20--chr20--NC_000020.9"
[21] "1--21--chr21--NC_000021.7" "1--22--chr22--NC_000022.9"
[23] "1--23--chrX--NC_000023.9" "1--24--chrY--NC_000024.8"
[25] "2--25--1--CM000663.1" "2--26--2--CM000664.1"
[27] "2--27--3--CM000665.1" "2--28--4--CM000666.1"
[29] "2--29--5--CM000667.1" "2--30--6--CM000668.1"
[31] "2--31--7--CM000669.1" "2--32--8--CM000670.1"
[33] "2--33--9--CM000671.1" "2--34--10--CM000672.1"
[35] "2--35--11--CM000673.1" "2--36--12--CM000674.1"
[37] "2--37--13--CM000675.1" "2--38--14--CM000676.1"
[39] "2--39--15--CM000677.1" "2--40--16--CM000678.1"
[41] "2--41--17--CM000679.1" "2--42--18--CM000680.1"
[43] "2--43--19--CM000681.1" "2--44--20--CM000682.1"
[45] "2--45--21--CM000683.1" "2--46--22--CM000684.1"
[47] "2--47--X--CM000685.1" "2--48--Y--CM000686.1"
[49] "2--49--MT--J01415.2" "3--50--chr1--CM000663.2"
[51] "3--51--chr2--CM000664.2" "3--52--chr3--CM000665.2"
[53] "3--53--chr4--CM000666.2" "3--54--chr5--CM000667.2"
[55] "3--55--chr6--CM000668.2" "3--56--chr7--CM000669.2"
[57] "3--57--chr8--CM000670.2" "3--58--chr9--CM000671.2"
[59] "3--59--chr10--CM000672.2" "3--60--chr11--CM000673.2"
[61] "3--61--chr12--CM000674.2" "3--62--chr13--CM000675.2"
[63] "3--63--chr14--CM000676.2" "3--64--chr15--CM000677.2"
[65] "3--65--chr16--CM000678.2" "3--66--chr17--CM000679.2"
[67] "3--67--chr18--CM000680.2" "3--68--chr19--CM000681.2"
[69] "3--69--chr20--CM000682.2" "3--70--chr21--CM000683.2"
[71] "3--71--chr22--CM000684.2" "3--72--chrX--CM000685.2"
[73] "3--73--chrY--CM000686.2" "3--74--chrM--J01415.2"
$select_input_data$dataset_types
[1] "Whole genome sequencing"
[2] "Exome sequencing"
[3] "Genotyping by array"
[4] "Transcriptome profiling by high-throughput sequencing"
[5] "Transcriptome profiling by array"
[6] "Amplicon sequencing"
[7] "Methylation binding domain sequencing"
[8] "Methylation profiling by high-throughput sequencing"
[9] "Phenotype information"
[10] "Study summary information"
[11] "Genomic variant calling"
[12] "Chromatin accessibility profiling by high-throughput sequencing"
[13] "Histone modification profiling by high-throughput sequencing"
[14] "Chip-Seq" The internal validation is a bit stricter in enforcing uniqueness of titles and descriptions for individual tables (the API itself doesn’t have this requirement). If the validation only fails in this particular case, you can still continue with creating the submission. However, there have been instances of failed reviews due to non-unique titles and descriptions before.
validation_summary <- default_validator(parsed_metadata)
validation_summary name items passes fails nNA error warning
1 study_is_na 1 1 0 0 FALSE FALSE
2 study_is_unique 1 1 0 0 FALSE FALSE
3 study_in_aliases 1 1 0 0 FALSE FALSE
4 study_all_aliases 1 1 0 0 FALSE FALSE
5 experiment_is_na 1 1 0 0 FALSE FALSE
6 experiment_is_unique 1 1 0 0 FALSE FALSE
7 experiment_in_aliases 1 1 0 0 FALSE FALSE
8 experiment_all_aliases 1 1 0 0 FALSE FALSE
9 alias_is_na 1 1 0 0 FALSE FALSE
10 alias_is_unique 1 1 0 0 FALSE FALSE
11 alias_in_aliases 1 1 0 0 FALSE FALSE
12 alias_all_aliases 1 1 0 0 FALSE FALSE
13 run_is_na 1 1 0 0 FALSE FALSE
14 run_is_unique 1 1 0 0 FALSE FALSE
15 run_in_aliases 1 1 0 0 FALSE FALSE
16 run_all_aliases 1 1 0 0 FALSE FALSE
17 dataset_is_na 1 1 0 0 FALSE FALSE
18 dataset_is_unique 1 1 0 0 FALSE FALSE
19 dataset_in_aliases 1 1 0 0 FALSE FALSE
20 dataset_all_aliases 1 1 0 0 FALSE FALSE
21 submission_title_is_na 1 1 0 0 FALSE FALSE
22 run_experiment_is_na 1 1 0 0 FALSE FALSE
23 run_sample_is_na 1 1 0 0 FALSE FALSE
24 run_file_type_is_na 1 1 0 0 FALSE FALSE
25 run_file_is_na 1 1 0 0 FALSE FALSE
26 run_file_is_unique 1 1 0 0 FALSE FALSE
27 run_experiment_in_aliases 1 1 0 0 FALSE FALSE
28 run_sample_in_aliases 1 1 0 0 FALSE FALSE
29 studies_title_is_unique 1 1 0 0 FALSE FALSE
30 studies_description_is_unique 1 1 0 0 FALSE FALSE
31 dataset_title_is_unique 1 1 0 0 FALSE FALSE
32 dataset_description_is_unique 1 1 0 0 FALSE FALSE
33 dataset_run_in_aliases 1 1 0 0 FALSE FALSE
34 dataset_all_aliases_in_run 1 1 0 0 FALSE FALSE
expression
1 !is.na(study)
2 is_unique(study)
3 study %vin% aliases[["studies"]]
4 aliases[["studies"]] %vin% study
5 !is.na(experiment)
6 is_unique(experiment)
7 experiment %vin% aliases[["experiments"]]
8 aliases[["experiments"]] %vin% experiment
9 !is.na(alias)
10 is_unique(alias)
11 alias %vin% aliases[["samples"]]
12 aliases[["samples"]] %vin% alias
13 !is.na(run)
14 is_unique(run)
15 run %vin% aliases[["runs"]]
16 aliases[["runs"]] %vin% run
17 !is.na(dataset)
18 is_unique(dataset)
19 dataset %vin% aliases[["datasets"]]
20 aliases[["datasets"]] %vin% dataset
21 !is.na(title)
22 !is.na(experiment)
23 !is.na(alias)
24 !is.na(run_file_type)
25 !is.na(files)
26 is_unique(unlist(files))
27 experiment %vin% aliases[["experiments"]]
28 alias %vin% aliases[["samples"]]
29 is_unique(title)
30 is_unique(description)
31 is_unique(title)
32 is_unique(description)
33 unlist(runs) %vin% aliases[["runs"]]
34 aliases[["runs"]] %vin% unlist(runs)Extract EGA API using the bundled YAML specification
api <- extract_api()Create a client using the embedded httr2 OAuth authentication (default).
ega <- create_client(api, verbosity = 0)Specify one of the available workflow function with your parsed metadata and a client as parameters.
responses <- new_submission(parsed_metadata, ega, "log.yaml")You can get the entire contents of current submission metadata via
get_submission workflow.
resp <- get_submission(00001, ega, logfile = "log.yaml")
resp <- get_submission(00001, ega)Or delete the entire contents of current submission metadata via
delete_submission_contents workflow or delete the entire submission by using
the delete_submission workflow.
resp <- delete_submission_contents(00001, ega)
resp <- delete_submission(00001, ega)Workflow for updating the submission metadata by PUT
method is under development.
Rega package supports authentication through OAuth or Bearer token via
functions ega_oauth (default) and ega_token respectively.
If you wish to create your own templates for EGA submissions, we provide a few functions to retrieve properties and enums through API and save them in text files. We will use the API and the client created above.
Relevant functions include:
get_schemas()get_properties()For testing, debugging and prototyping purposes, it is possible to directly use generated bearer token with API when creating the client. It is then your responsibility of the user to track the validity and refresh the token as necessary.
bt <- ega_token()
ega <- create_client(api, bt$access_token)
ega$get__enums()sessionInfo()R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS
Matrix products: default
BLAS: /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
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
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rega_0.99.1 knitr_1.50 BiocStyle_2.37.0
loaded via a namespace (and not attached):
[1] jsonlite_2.0.0 dplyr_1.1.4 compiler_4.5.0
[4] BiocManager_1.30.26 tidyselect_1.2.1 validate_1.1.5
[7] stringr_1.5.1 tidyr_1.3.1 jquerylib_0.1.4
[10] yaml_2.3.10 fastmap_1.2.0 readxl_1.4.5
[13] jsonvalidate_1.5.0 R6_2.6.1 generics_0.1.4
[16] httr2_1.1.2 tibble_3.2.1 bookdown_0.43
[19] bslib_0.9.0 pillar_1.10.2 rlang_1.1.6
[22] utf8_1.2.5 cachem_1.1.0 stringi_1.8.7
[25] xfun_0.52 sass_0.4.10 cli_3.6.5
[28] magrittr_2.0.3 digest_0.6.37 grid_4.5.0
[31] settings_0.2.7 rappdirs_0.3.3 askpass_1.2.1
[34] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.3
[37] glue_1.8.0 cellranger_1.1.0 rmarkdown_2.29
[40] purrr_1.0.4 tools_4.5.0 pkgconfig_2.0.3
[43] htmltools_0.5.8.1