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Getting Started


Author: Brian M. Schilder


Updated: Mar-16-2026

Source: vignettes/echodeps.Rmd
echodeps.Rmd

Gather package metadata

echoverse

package_metadata pulls metadata from the DESCRIPTION files from a package (or list of packages) and organises them into a convenient table.

Metadata for the echoverse suite of R packages will be retrieved by default. While echoverse itself is not the name of an R package, package_metadata will automatically recognise this special command and retrieve all packages that are part of this suite.

meta_echoverse <- echodeps::package_metadata(pkgs = "echoverse")
## Adding all echoverse modules to metadata search.
## Collecting metadata for 14 packages
knitr::kable(meta_echoverse)
package owner repo authors github_url package Type Title Version Date Description License URL BugReports Encoding Depends biocViews Imports Suggests Remotes RoxygenNote VignetteBuilder Config/testthat/edition RemoteType RemoteHost RemoteRepo RemoteUsername RemoteRef RemoteSha GithubRepo GithubUsername GithubRef GithubSHA1 NeedsCompilation Packaged Author Maintainer Built LazyData SystemRequirements StagedInstall Config/reticulate owner_repo ref
catalogueR RajLabMSSM catalogueR Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/catalogueR catalogueR Package QTL Data Extraction and Colocalization 2.0.1 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Rapid querying, colocalization, and plotting of summary stats from the eQTL Catalogue https://www.ebi.ac.uk/eqtl/. eQTL Catalogue currently contains >100 datasets from 20 different studies (including GTEx), across many tissues/cell types/conditions. GPL-3 https://github.com/RajLabMSSM/catalogueR https://github.com/RajLabMSSM/catalogueR/issues UTF-8 R (>= 4.1) echodata, echotabix, dplyr, tidyr, data.table, piggyback, parallel, ggplot2, ggrepel, patchwork, scales, jsonlite, coloc, AnnotationDbi, EnsDb.Hsapiens.v75, GenomicRanges, downloadR echoLD, markdown, rmarkdown, magick, methods, devtools, badger, BiocStyle, knitr, testthat (>= 3.0.0) github::RajLabMSSM/echotabix, github::RajLabMSSM/echodata, github::RajLabMSSM/echoLD, github::RajLabMSSM/downloadR 7.3.3 knitr 3 github api.github.com catalogueR RajLabMSSM HEAD d7b712644f51825165086abc2a0613a9618398ba catalogueR RajLabMSSM HEAD d7b712644f51825165086abc2a0613a9618398ba no 2026-03-14 17:37:28 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:37:28 UTC; unix true NA NA NA RajLabMSSM/catalogueR RajLabMSSM/catalogueR
devoptera RajLabMSSM devoptera Brian Schilder https://github.com/RajLabMSSM/devoptera devoptera Package Practical Tools for R Developers 1.0.0 2026-03-08 Brian Schilder Echoverse module: Practical tools for R developers. GPL-3 https://github.com/RajLabMSSM/devoptera https://github.com/RajLabMSSM/devoptera/issues UTF-8 R (>= 4.1) Software, Genetics, FunctionalGenomics, SystemsBiology rlang, devtools, BiocCheck, methods, here, data.table, R.utils, rstudioapi rworkflows, rmarkdown, testthat, covr, BiocStyle, ggimage, ggplot2, knitr, markdown, hexSticker github::neurogenomics/rworkflows 7.3.3 knitr 3 github api.github.com devoptera RajLabMSSM HEAD 1356e00354d581883acf7700df9b4ba879c76243 devoptera RajLabMSSM HEAD 1356e00354d581883acf7700df9b4ba879c76243 no 2026-03-14 17:38:58 UTC; root Brian Schilder Brian Schilder R 4.6.0; ; 2026-03-14 17:38:58 UTC; unix NA NA NA NA RajLabMSSM/devoptera RajLabMSSM/devoptera
downloadR RajLabMSSM downloadR Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/downloadR downloadR Package Echoverse Module: Single- and Multi-Threaded Downloading Functions 1.0.0 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Echoverse module: Single- and multi-threaded downloading functions. GPL (>= 3) https://github.com/RajLabMSSM/downloadR https://github.com/RajLabMSSM/downloadR/issues UTF-8 R (>= 4.1) echoconda, utils, stats, methods, jsonlite, data.table, aws.s3 markdown, rmarkdown, remotes, knitr, BiocStyle, covr, testthat (>= 3.0.0), badger, zen4R github::RajLabMSSM/echoconda 7.3.3 knitr 3 github api.github.com downloadR RajLabMSSM HEAD a0f5420ecb82e1a0912e1f30fde051c9f501d199 downloadR RajLabMSSM HEAD a0f5420ecb82e1a0912e1f30fde051c9f501d199 no 2026-03-14 17:34:33 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:34:34 UTC; unix NA NA NA NA RajLabMSSM/downloadR RajLabMSSM/downloadR
echoLD RajLabMSSM echoLD Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/echoLD echoLD Package Echoverse Module: LD Downloading and Processing 1.0.0 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Echoverse module: LD downloading and processing. GPL (>= 3) https://github.com/RajLabMSSM/echoLD https://github.com/RajLabMSSM/echoLD/issues UTF-8 R (>= 4.1) echotabix, downloadR, echodata, echoconda, dplyr, methods, Matrix, data.table, reticulate, GenomicRanges, VariantAnnotation, snpStats, tools markdown, rmarkdown, remotes, knitr, BiocStyle, covr, testthat (>= 3.0.0), gaston, graphics, LDlinkR, adjclust, badger, parallel github::RajLabMSSM/echotabix, github::RajLabMSSM/downloadR, github::RajLabMSSM/echodata, github::RajLabMSSM/echoconda 7.3.3 knitr 3 github api.github.com echoLD RajLabMSSM HEAD 12d903b662f3acb43b9df21b1eb0a1343a57380a echoLD RajLabMSSM HEAD 12d903b662f3acb43b9df21b1eb0a1343a57380a no 2026-03-14 17:35:46 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:35:46 UTC; unix true Python (>= 3.7.0) NA list( packages = list( list(package = “pandas”) ) ) RajLabMSSM/echoLD RajLabMSSM/echoLD
echoannot RajLabMSSM echoannot Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/echoannot echoannot Package Echoverse Module: Annotate Fine-Mapping Results 1.0.1 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Echoverse module: Functions for annotating genomic data with annotations and epigenomic data. GPL-3 https://github.com/RajLabMSSM/echoannot https://github.com/RajLabMSSM/echoannot/issues UTF-8 R (>= 4.1) Genetics, FunctionalGenomics, SystemsBiology echodata, echotabix, downloadR, dplyr, stringr, data.table, utils, tools, methods, stats, tidyr, parallel, ggplot2, patchwork, ggbio, GenomicRanges, DescTools, grDevices, rtracklayer, S4Vectors, BiocGenerics, IRanges XGR, markdown, rmarkdown, remotes, knitr, BiocStyle, badger, covr, testthat (>= 3.0.0), corrplot, pheatmap, haploR, biomaRt, regioneR, motifbreakR, MotifDb, BSgenome, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BiocParallel github::RajLabMSSM/echodata, github::RajLabMSSM/echotabix, github::RajLabMSSM/downloadR 7.3.3 knitr 3 github api.github.com echoannot RajLabMSSM HEAD b00ff996bac7e7327f60c0513b3bd4296532bf6a echoannot RajLabMSSM HEAD b00ff996bac7e7327f60c0513b3bd4296532bf6a no 2026-03-14 17:34:52 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:34:53 UTC; unix true NA NA NA RajLabMSSM/echoannot RajLabMSSM/echoannot
echoconda RajLabMSSM echoconda Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/echoconda echoconda Package Echoverse Module: Conda Environment Management 1.0.0 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Various utility functions to find, build, and use conda environments from within R. GPL (>= 3) https://github.com/RajLabMSSM/echoconda https://github.com/RajLabMSSM/echoconda/issues UTF-8 R (>= 4.1) utils, methods, R.utils, data.table, dplyr, yaml, stringr, reticulate (>= 1.24), basilisk, basilisk.utils, echodata markdown, rmarkdown, magick, remotes, knitr, BiocStyle, covr, testthat (>= 3.0.0), badger, hexSticker, parallel, readr, tidyr, microbenchmark, genetics.binaRies github::MRCIEU/genetics.binaRies, github::RajLabMSSM/echodata 7.3.3 knitr 3 github api.github.com echoconda RajLabMSSM HEAD 3d16d5d075db122f8b896b98eda8dabfb69d6bf9 echoconda RajLabMSSM HEAD 3d16d5d075db122f8b896b98eda8dabfb69d6bf9 no 2026-03-14 17:33:54 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:33:56 UTC; unix NA NA no NA RajLabMSSM/echoconda RajLabMSSM/echoconda
echodata RajLabMSSM echodata Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/echodata echodata Package Echoverse Module: Fine-Mapping Data Access and Formatting 1.0.0 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Echoverse module: Examples of fine-mapped GWAS summary statistics, data formatting functions, and API access to the echolocatoR Fine-mapping Portal. GPL-3 https://github.com/RajLabMSSM/echodata https://github.com/RajLabMSSM/echodata/issues UTF-8 R (>= 4.1) Genetics, FunctionalGenomics, SystemsBiology dplyr, data.table, R.utils, methods, utils, tools, tidyr, parallel, openxlsx, DT, readr, piggyback, MungeSumstats (>= 1.3.14) markdown, rmarkdown, remotes, knitr, BiocStyle, covr, testthat (>= 3.0.0), htmltools, badger, BSgenome, GenomicRanges, GenomeInfoDb, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, biomaRt, arrow, ggplot2, echogithub, orthogene github::RajLabMSSM/echogithub 7.3.3 knitr 3 github api.github.com echodata RajLabMSSM HEAD 5aff7fc56f17cc77f99f905aa8bb12ac386129d3 echodata RajLabMSSM HEAD 5aff7fc56f17cc77f99f905aa8bb12ac386129d3 no 2026-03-14 17:33:22 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:33:23 UTC; unix true xml2 NA NA RajLabMSSM/echodata RajLabMSSM/echodata
echodeps RajLabMSSM echodeps Brian Schilder https://github.com/RajLabMSSM/echodeps echodeps Package Echoverse Module: Create Package Dependency Graphs 1.0.0 2026-03-08 Brian Schilder Echoverse module: Create package dependency graphs. GPL-3 https://github.com/RajLabMSSM/echodeps https://github.com/RajLabMSSM/echodeps/issues UTF-8 R (>= 4.1) Genetics, FunctionalGenomics, SystemsBiology rworkflows, methods, data.table, tidygraph, igraph, pkgnet, visNetwork, devtools, tools, pals, echogithub echolocatoR, echodata, echotabix, echoannot, echoconda, echoLD, echoplot, catalogueR, echofinemap, downloadR, echoverseTemplate, devoptera, markdown, rmarkdown, remotes, knitr, BiocStyle, covr, testthat (>= 3.0.0), utils, dplyr, webshot2 github::RajLabMSSM/echogithub, github::RajLabMSSM/echodata, github::RajLabMSSM/echotabix, github::RajLabMSSM/downloadR, github::RajLabMSSM/echoannot, github::RajLabMSSM/echoconda, github::RajLabMSSM/echoLD, github::RajLabMSSM/echoplot, github::RajLabMSSM/catalogueR, github::RajLabMSSM/echofinemap, github::RajLabMSSM/echoverseTemplate, github::RajLabMSSM/devoptera, github::RajLabMSSM/echolocatoR, github::neurogenomics/rworkflows 7.3.3 knitr 3 NA NA NA NA NA NA NA NA NA NA NA NA Brian Schilder Brian Schilder R 4.6.0; ; 2026-03-16 05:28:21 UTC; unix NA NA NA NA RajLabMSSM/echodeps RajLabMSSM/echodeps
echofinemap RajLabMSSM echofinemap Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/echofinemap echofinemap Package Echoverse Module: Fine-Mapping Functions 1.0.0 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Echoverse module: Statistical and functional fine-mapping functions. GPL-3 https://github.com/RajLabMSSM/echofinemap https://github.com/RajLabMSSM/echofinemap/issues UTF-8 R (>= 4.1) Genetics, FunctionalGenomics, SystemsBiology echodata, echoconda, echoannot, echoLD, coloc, tools, methods, stringr, R.utils, data.table, dplyr, tidyr, cli, rlang, Matrix, susieR (>= 0.12.0), downloadR Rfast, markdown, rmarkdown, magick, remotes, knitr, BiocStyle, covr, testthat (>= 3.0.0), badger, hexSticker, ggpubr, ggrepel, patchwork, purrr, devtools, genetics.binaRies, Ckmeans.1d.dp github::RajLabMSSM/echodata, github::RajLabMSSM/echoLD, github::RajLabMSSM/echoannot, github::RajLabMSSM/echoconda, github::MRCIEU/genetics.binaRies, github::RajLabMSSM/downloadR 7.3.3 knitr 3 github api.github.com echofinemap RajLabMSSM HEAD d13b9af9cc9facda54074f665c61847d09d9e496 echofinemap RajLabMSSM HEAD d13b9af9cc9facda54074f665c61847d09d9e496 no 2026-03-14 17:38:03 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:38:04 UTC; unix NA NA NA NA RajLabMSSM/echofinemap RajLabMSSM/echofinemap
echogithub RajLabMSSM echogithub Brian Schilder, Jack Humphrey, Towfique Raj, Hiranyamaya Dash https://github.com/RajLabMSSM/echogithub echogithub Package Echoverse Module: Extract Data and Metadata from GitHub 1.0.0 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj, Hiranyamaya Dash Echoverse module: Extract data and metadata from GitHub. GPL-3 https://github.com/RajLabMSSM/echogithub https://github.com/RajLabMSSM/echogithub/issues UTF-8 R (>= 4.1) Genetics, FunctionalGenomics, SystemsBiology utils, methods, stats, gh, data.table, stringr, RCurl, rvest, parallel, rworkflows markdown, rmarkdown, testthat (>= 3.0.0), remotes, knitr, BiocStyle, covr, httr, BiocManager, githubinstall, UpSetR, grDevices, dlstats (>= 0.1.6), cranlogs, BiocPkgTools github::neurogenomics/cranlogs, github::neurogenomics/rworkflows, github::hoxo-m/githubinstall 7.3.3 knitr 3 github api.github.com echogithub RajLabMSSM HEAD 11da90a9fb9f8d8357975f628465cdb015e746e7 echogithub RajLabMSSM HEAD 11da90a9fb9f8d8357975f628465cdb015e746e7 no 2026-03-14 17:31:40 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj, Hiranyamaya Dash Brian Schilder R 4.6.0; ; 2026-03-14 17:31:41 UTC; unix NA NA NA NA RajLabMSSM/echogithub RajLabMSSM/echogithub
echolocatoR RajLabMSSM echolocatoR Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/echolocatoR echolocatoR Package Automated Genomic Fine-Mapping 3.0.0 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Automated statistical and functional fine-mapping with extensive access to genome-wide datasets. GPL-3 https://github.com/RajLabMSSM/echolocatoR https://github.com/RajLabMSSM/echolocatoR/issues UTF-8 R (>= 4.1) Genetics, FunctionalGenomics, SystemsBiology echoconda, downloadR, echodata, echotabix, echoannot, catalogueR, echoLD, echofinemap, echoplot, data.table, methods, stringr, lifecycle, cli, utf8, scales MungeSumstats (>= 1.3.14), echodeps, echogithub, BiocStyle, remotes, rmarkdown, knitr, testthat (>= 3.0.0), ggplot2, patchwork, rworkflows github::RajLabMSSM/echoconda, github::RajLabMSSM/downloadR, github::RajLabMSSM/echogithub, github::RajLabMSSM/echodata, github::RajLabMSSM/echotabix, github::RajLabMSSM/echoannot, github::RajLabMSSM/catalogueR, github::RajLabMSSM/echoLD, github::RajLabMSSM/echofinemap, github::RajLabMSSM/echoplot, github::RajLabMSSM/echodeps, github::neurogenomics/rworkflows 7.3.3 knitr 3 github api.github.com echolocatoR RajLabMSSM HEAD 6e20d184298cb60ac33a888283f78f380ebc5974 echolocatoR RajLabMSSM HEAD 6e20d184298cb60ac33a888283f78f380ebc5974 no 2026-03-14 17:39:09 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:39:09 UTC; unix NA NA NA NA RajLabMSSM/echolocatoR RajLabMSSM/echolocatoR
echoplot RajLabMSSM echoplot Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/echoplot echoplot Package Echoverse Module: Locus Plot Creation for Fine-Mapping and Colocalization Studies 1.0.0 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Echoverse module: Locus plot creation for fine-mapping and colocalization studies. GPL-3 https://github.com/RajLabMSSM/echoplot https://github.com/RajLabMSSM/echoplot/issues UTF-8 R (>= 4.1) Genetics, FunctionalGenomics, SystemsBiology echodata, echoannot, echoLD, methods, ggplot2, ggbio, ggrepel, ggnewscale, stats, patchwork, DescTools, GenomicRanges, EnsDb.Hsapiens.v75, ensembldb, AnnotationFilter, GenomicFeatures, S4Vectors, data.table, dplyr, pals, rlang rworkflows, markdown, rmarkdown, magick, remotes, knitr, BiocStyle, covr, testthat (>= 3.0.0), badger, hexSticker, utils, Gviz, stringr github::RajLabMSSM/echodata, github::RajLabMSSM/echoannot, github::RajLabMSSM/echoLD 7.3.3 knitr 3 github api.github.com echoplot RajLabMSSM HEAD 45041697a9d96cf1ef8141b42a01ce60bc5da056 echoplot RajLabMSSM HEAD 45041697a9d96cf1ef8141b42a01ce60bc5da056 no 2026-03-14 17:36:33 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:36:33 UTC; unix NA NA NA NA RajLabMSSM/echoplot RajLabMSSM/echoplot
echotabix RajLabMSSM echotabix Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/echotabix echotabix Package Echoverse Module: Automated Creation and Querying of Tabix Files 1.0.1 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Converts genomic data files to tabix format (including liftover, sorting, compression, and indexing steps) with a single function. Retrieves local or remote tabix VCF/tabular files with helper functions for creating queries from subsets of genomic data (e.g GWAS/QTL loci, genomic ranges). Multiple methods available at each step, including wrapper functions for an up-to-date, conda-based installation of htslib tools. GPL (>= 3) https://github.com/RajLabMSSM/echotabix https://github.com/RajLabMSSM/echotabix/issues UTF-8 R (>= 4.1) echodata, echoconda, utils, R.utils, tools, dplyr, methods, data.table, GenomeInfoDb, IRanges, GenomicRanges, Biostrings, VariantAnnotation, Rsamtools, rtracklayer, MungeSumstats (>= 1.3.14), BiocManager, BiocGenerics markdown, rmarkdown, knitr, BiocStyle, covr, testthat (>= 3.0.0), remotes, parallel, badger, seqminer, GenomicFiles github::RajLabMSSM/echodata, github::RajLabMSSM/echoconda 7.3.3 knitr 3 github api.github.com echotabix RajLabMSSM HEAD 16b5eae83572e87af7cfd19fd19240fbe5536be5 echotabix RajLabMSSM HEAD 16b5eae83572e87af7cfd19fd19240fbe5536be5 no 2026-03-14 17:34:00 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:34:01 UTC; unix NA Python (>= 3.7.0) NA NA RajLabMSSM/echotabix RajLabMSSM/echotabix
echoverseTemplate RajLabMSSM echoverseTemplate Brian Schilder, Jack Humphrey, Towfique Raj https://github.com/RajLabMSSM/echoverseTemplate echoverseTemplate Package Echoverse Module: echoversePackageTitle 1.0.0 2026-03-08 Brian Schilder, Jack Humphrey, Towfique Raj Echoverse module: echoversePackageDescription. GPL-3 https://github.com/RajLabMSSM/echoverseTemplate https://github.com/RajLabMSSM/echoverseTemplate/issues UTF-8 R (>= 4.1) Software, Genetics, FunctionalGenomics, SystemsBiology rworkflows, markdown, rmarkdown, remotes, knitr, BiocStyle, covr, testthat (>= 3.0.0), utils, rlang, methods github::neurogenomics/rworkflows 7.2.3 knitr 3 github api.github.com echoverseTemplate RajLabMSSM HEAD 8fbb7e7b7fafca6a7c3a9475ef2232a140c3179d echoverseTemplate RajLabMSSM HEAD 8fbb7e7b7fafca6a7c3a9475ef2232a140c3179d no 2026-03-14 17:38:43 UTC; root Brian Schilder, Jack Humphrey, Towfique Raj Brian Schilder R 4.6.0; ; 2026-03-14 17:38:43 UTC; unix NA NA NA NA RajLabMSSM/echoverseTemplate RajLabMSSM/echoverseTemplate

dplyr

You can use the same function to retrieve metadata for any CRAN or Bioconductor package.

meta <- echodeps::package_metadata(pkgs = c("dplyr","data.table","igraph"))
## Collecting metadata for 3 packages
knitr::kable(meta)
package owner repo authors github_url Type package Title Version Description License URL BugReports Depends Imports Suggests VignetteBuilder Config/build/compilation-database Config/Needs/website Config/testthat/edition Encoding LazyData RoxygenNote NeedsCompilation Packaged Author Maintainer Repository Date/Publication Built ByteCompile Enhances LinkingTo Config/build/never-clean Config/comment/compilation-database Config/Needs/build Config/Needs/coverage Config/testthat/parallel Config/testthat/start-first SystemRequirements owner_repo ref
data.table Rdatatable data.table Tyson Barrett, Matt Dowle, Arun Srinivasan, Jan Gorecki, Michael Chirico, Toby Hocking, Benjamin Schwendinger, Ivan Krylov, Pasha Stetsenko, Tom Short, Steve Lianoglou, Eduard Antonyan, Markus Bonsch, Hugh Parsonage, Scott Ritchie, Kun Ren, Xianying Tan, Rick Saporta, Otto Seiskari, Xianghui Dong, Michel Lang, Watal Iwasaki, Seth Wenchel, Karl Broman, Tobias Schmidt, David Arenburg, Ethan Smith, Francois Cocquemas, Matthieu Gomez, Philippe Chataignon, Nello Blaser, Dmitry Selivanov, Andrey Riabushenko, Cheng Lee, Declan Groves, Daniel Possenriede, Felipe Parages, Denes Toth, Mus Yaramaz-David, Ayappan Perumal, James Sams, Martin Morgan, Michael Quinn, @javrucebo, Marc Halperin, Roy Storey, Manish Saraswat, Morgan Jacob, Michael Schubmehl, Davis Vaughan, Leonardo Silvestri, Jim Hester, Anthony Damico, Sebastian Freundt, David Simons, Elliott Sales de Andrade, Cole Miller, Jens Peder Meldgaard, Vaclav Tlapak, Kevin Ushey, Dirk Eddelbuettel, Tony Fischetti, Ofek Shilon, Vadim Khotilovich, Hadley Wickham, Bennet Becker, Kyle Haynes, Boniface Christian Kamgang, Olivier Delmarcell, Josh O’Brien, Dereck de Mezquita, Michael Czekanski, Dmitry Shemetov, Nitish Jha, Joshua Wu, Iago Giné-Vázquez, Anirban Chetia, Doris Amoakohene, Angel Feliz, Michael Young, Mark Seeto, Philippe Grosjean, Vincent Runge, Christian Wia, Elise Maigné, Vincent Rocher, Vijay Lulla, Aljaž Sluga, Bill Evans, Reino Bruner, @badasahog, Vinit Thakur, Mukul Kumar, Ildikó Czeller, Manmita Das https://github.com/Rdatatable/data.table NA data.table Extension of data.frame 1.18.2.1 Tyson Barrett, Matt Dowle, Arun Srinivasan, Jan Gorecki, Michael Chirico, Toby Hocking, Benjamin Schwendinger, Ivan Krylov, Pasha Stetsenko, Tom Short, Steve Lianoglou, Eduard Antonyan, Markus Bonsch, Hugh Parsonage, Scott Ritchie, Kun Ren, Xianying Tan, Rick Saporta, Otto Seiskari, Xianghui Dong, Michel Lang, Watal Iwasaki, Seth Wenchel, Karl Broman, Tobias Schmidt, David Arenburg, Ethan Smith, Francois Cocquemas, Matthieu Gomez, Philippe Chataignon, Nello Blaser, Dmitry Selivanov, Andrey Riabushenko, Cheng Lee, Declan Groves, Daniel Possenriede, Felipe Parages, Denes Toth, Mus Yaramaz-David, Ayappan Perumal, James Sams, Martin Morgan, Michael Quinn, @javrucebo, Marc Halperin, Roy Storey, Manish Saraswat, Morgan Jacob, Michael Schubmehl, Davis Vaughan, Leonardo Silvestri, Jim Hester, Anthony Damico, Sebastian Freundt, David Simons, Elliott Sales de Andrade, Cole Miller, Jens Peder Meldgaard, Vaclav Tlapak, Kevin Ushey, Dirk Eddelbuettel, Tony Fischetti, Ofek Shilon, Vadim Khotilovich, Hadley Wickham, Bennet Becker, Kyle Haynes, Boniface Christian Kamgang, Olivier Delmarcell, Josh O’Brien, Dereck de Mezquita, Michael Czekanski, Dmitry Shemetov, Nitish Jha, Joshua Wu, Iago Giné-Vázquez, Anirban Chetia, Doris Amoakohene, Angel Feliz, Michael Young, Mark Seeto, Philippe Grosjean, Vincent Runge, Christian Wia, Elise Maigné, Vincent Rocher, Vijay Lulla, Aljaž Sluga, Bill Evans, Reino Bruner, @badasahog, Vinit Thakur, Mukul Kumar, Ildikó Czeller, Manmita Das Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development. MPL-2.0 | file LICENSE https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table https://github.com/Rdatatable/data.table/issues R (>= 3.4.0) methods bit64 (>= 4.0.0), bit (>= 4.0.4), R.utils (>= 2.13.0), xts, zoo (>= 1.8-1), yaml, knitr, markdown knitr NA NA NA UTF-8 NA NA yes 2026-01-25 04:12:25 UTC; tysonbarrett Tyson Barrett, Matt Dowle, Arun Srinivasan, Jan Gorecki, Michael Chirico, Toby Hocking, Benjamin Schwendinger, Ivan Krylov, Pasha Stetsenko, Tom Short, Steve Lianoglou, Eduard Antonyan, Markus Bonsch, Hugh Parsonage, Scott Ritchie, Kun Ren, Xianying Tan, Rick Saporta, Otto Seiskari, Xianghui Dong, Michel Lang, Watal Iwasaki, Seth Wenchel, Karl Broman, Tobias Schmidt, David Arenburg, Ethan Smith, Francois Cocquemas, Matthieu Gomez, Philippe Chataignon, Nello Blaser, Dmitry Selivanov, Andrey Riabushenko, Cheng Lee, Declan Groves, Daniel Possenriede, Felipe Parages, Denes Toth, Mus Yaramaz-David, Ayappan Perumal, James Sams, Martin Morgan, Michael Quinn, @javrucebo, Marc Halperin, Roy Storey, Manish Saraswat, Morgan Jacob, Michael Schubmehl, Davis Vaughan, Leonardo Silvestri, Jim Hester, Anthony Damico, Sebastian Freundt, David Simons, Elliott Sales de Andrade, Cole Miller, Jens Peder Meldgaard, Vaclav Tlapak, Kevin Ushey, Dirk Eddelbuettel, Tony Fischetti, Ofek Shilon, Vadim Khotilovich, Hadley Wickham, Bennet Becker, Kyle Haynes, Boniface Christian Kamgang, Olivier Delmarcell, Josh O’Brien, Dereck de Mezquita, Michael Czekanski, Dmitry Shemetov, Nitish Jha, Joshua Wu, Iago Giné-Vázquez, Anirban Chetia, Doris Amoakohene, Angel Feliz, Michael Young, Mark Seeto, Philippe Grosjean, Vincent Runge, Christian Wia, Elise Maigné, Vincent Rocher, Vijay Lulla, Aljaž Sluga, Bill Evans, Reino Bruner, @badasahog, Vinit Thakur, Mukul Kumar, Ildikó Czeller, Manmita Das Tyson Barrett CRAN 2026-01-27 11:40:15 UTC R 4.6.0; x86_64-pc-linux-gnu; 2026-02-11 19:35:39 UTC; unix TRUE NA NA NA NA NA NA NA NA NA Rdatatable/data.table Rdatatable/data.table
dplyr tidyverse dplyr Hadley Wickham, Romain François, Lionel Henry, Kirill Müller, Davis Vaughan, Posit Software, PBC https://github.com/tidyverse/dplyr Package dplyr A Grammar of Data Manipulation 1.2.0 Hadley Wickham, Romain François, Lionel Henry, Kirill Müller, Davis Vaughan, Posit Software, PBC A fast, consistent tool for working with data frame like objects, both in memory and out of memory. MIT + file LICENSE https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr https://github.com/tidyverse/dplyr/issues R (>= 4.1.0) cli (>= 3.6.2), generics, glue (>= 1.3.2), lifecycle (>= 1.0.5), magrittr (>= 1.5), methods, pillar (>= 1.9.0), R6, rlang (>= 1.1.7), tibble (>= 3.2.0), tidyselect (>= 1.2.0), utils, vctrs (>= 0.7.1) broom, covr, DBI, dbplyr (>= 2.2.1), ggplot2, knitr, Lahman, lobstr, nycflights13, purrr, rmarkdown, RSQLite, stringi (>= 1.7.6), testthat (>= 3.1.5), tidyr (>= 1.3.0), withr knitr true tidyverse/tidytemplate 3 UTF-8 true 7.3.3 yes 2026-01-30 23:05:30 UTC; hadleywickham Hadley Wickham, Romain François, Lionel Henry, Kirill Müller, Davis Vaughan, Posit Software, PBC Hadley Wickham CRAN 2026-02-03 08:50:47 UTC R 4.6.0; x86_64-pc-linux-gnu; 2026-02-11 19:53:08 UTC; unix NA NA NA NA NA NA NA NA NA NA tidyverse/dplyr tidyverse/dplyr
igraph igraph rigraph Gábor Csárdi, Tamás Nepusz, Vincent Traag, Szabolcs Horvát, Fabio Zanini, Daniel Noom, Kirill Müller, Michael Antonov, Chan Zuckerberg Initiative, David Schoch, Maëlle Salmon https://github.com/igraph/rigraph NA igraph Network Analysis and Visualization 2.2.2 Gábor Csárdi, Tamás Nepusz, Vincent Traag, Szabolcs Horvát, Fabio Zanini, Daniel Noom, Kirill Müller, Michael Antonov, Chan Zuckerberg Initiative, David Schoch, Maëlle Salmon Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more. GPL (>= 2) https://r.igraph.org/, https://igraph.org/, https://igraph.discourse.group/ https://github.com/igraph/rigraph/issues methods, R (>= 3.5.0) cli, graphics, grDevices, lifecycle, magrittr, Matrix, pkgconfig (>= 2.0.0), rlang (>= 1.1.0), stats, utils, vctrs ape (>= 5.7-0.1), callr, decor, digest, igraphdata, knitr, rgl (>= 1.3.14), rmarkdown, scales, stats4, tcltk, testthat, vdiffr, withr knitr false here, readr, tibble, xmlparsedata, xml2 3 UTF-8 NA 7.3.3.9000 yes 2026-02-12 09:58:29 UTC; kirill Gábor Csárdi, Tamás Nepusz, Vincent Traag, Szabolcs Horvát, Fabio Zanini, Daniel Noom, Kirill Müller, Michael Antonov, Chan Zuckerberg Initiative, David Schoch, Maëlle Salmon Kirill Müller CRAN 2026-02-12 14:00:12 UTC R 4.6.0; x86_64-pc-linux-gnu; 2026-03-14 17:39:57 UTC; unix NA graph cpp11 (>= 0.5.0) true Generate manually with pkgload:::generate_db() for faster pkgload::load_all() r-lib/roxygen2, devtools, irlba, pkgconfig, igraph/igraph.r2cdocs, moodymudskipper/devtag covr true aaa-auto, vs-es, scan, vs-operators, weakref, watts.strogatz.game libxml2 (optional), glpk (>= 4.57, optional) igraph/rigraph igraph/rigraph

Create a dependency graph

dep_graph builds upon the above functions and creates a dependency graph for all the dependencies of a given R package (or a selected subset of its dependencies).

Metadata for each package is automatically extracted and shown as tooltips that appear when you hover over the respective node.

All of the plots, graphs, metadata, and saved file paths generated by dep_graph are returned to the user as a named list in case they would like to explore them further.

echolocatoR 

res_echoverse <- echodeps::dep_graph(pkg = "echolocatoR",
                                     ## Setting show_plot for vignette purposes
                                     show_plot = list(r=TRUE,
                                                      browser=FALSE))

dplyr 

res <- echodeps::dep_graph(pkg = "dplyr",
                           shape = "hexagon",
                           layout = function(graph, pkg){
                               visNetwork::visIgraphLayout(
                                   graph = graph,
                                   layout = "layout_nicely"
                               )
                           }
                           )

Session Info 

utils::sessionInfo()
## R Under development (unstable) (2026-03-12 r89607)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [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: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] echodeps_1.0.0   BiocStyle_2.39.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6        xfun_0.56           bslib_0.10.0       
##  [4] ggplot2_4.0.2       htmlwidgets_1.6.4   visNetwork_2.1.4   
##  [7] gh_1.5.0            vctrs_0.7.1         tools_4.6.0        
## [10] bitops_1.0-9        generics_0.1.4      yulab.utils_0.2.4  
## [13] parallel_4.6.0      tibble_3.3.1        pkgconfig_2.0.3    
## [16] data.table_1.18.2.1 RColorBrewer_1.1-3  S7_0.2.1           
## [19] desc_1.4.3          pals_1.10           lifecycle_1.0.5    
## [22] compiler_4.6.0      farver_2.1.2        stringr_1.6.0      
## [25] dlstats_0.1.7       textshaping_1.0.5   mapproj_1.2.12     
## [28] htmltools_0.5.9     maps_3.4.3          sass_0.4.10        
## [31] RCurl_1.98-1.17     yaml_2.3.12         pkgdown_2.2.0      
## [34] pillar_1.11.1       jquerylib_0.1.4     tidyr_1.3.2        
## [37] cachem_1.1.0        tidyselect_1.2.1    digest_0.6.39      
## [40] stringi_1.8.7       dplyr_1.2.0         purrr_1.2.1        
## [43] bookdown_0.46       rprojroot_2.1.1     fastmap_1.2.0      
## [46] grid_4.6.0          here_1.0.2          colorspace_2.1-2   
## [49] cli_3.6.5           magrittr_2.0.4      dichromat_2.0-0.1  
## [52] tidygraph_1.3.1     scales_1.4.0        rappdirs_0.3.4     
## [55] rmarkdown_2.30      rvcheck_0.2.1       igraph_2.2.2       
## [58] otel_0.2.0          ragg_1.5.1          evaluate_1.0.5     
## [61] echogithub_1.0.0    knitr_1.51          rworkflows_1.0.8   
## [64] rlang_1.1.7         glue_1.8.0          BiocManager_1.30.27
## [67] renv_1.1.8          jsonlite_2.0.0      R6_2.6.1           
## [70] badger_0.2.5        systemfonts_1.3.2   fs_1.6.7