R packages by L. Collado-Torres

Lieber Institute for Brain Development, Johns Hopkins Medical CampusCenter for Computational Biology, Johns Hopkins University
lcolladotor@gmail.com

Abstract

I like to check my R packages using GitHub Actions, Bioconductor and other tools. This small website helps me see the status of the packages I’ve made without having to navigate to a bunch of other websites. This website also helps me keep track of project repositories I’ve made where users might ask questions.

Bioconductor

Maintainer

Software

• biocthis

• derfinder

• derfinderHelper

• derfinderPlot

• megadepth

• recount

• recount3

• regionReport

Annotation

• GenomicState

Experiment data

• derfinderData

• spatialLIBD

Workflow

• recountWorkflow

Contributor

• DeconvoBuddies

• qsvaR

• smokingMouse

• TREG

• visiumStitched

CDSB Mexico

• regutools

GitHub

Actively maintained

• BestPracticesST

• jaffelab

Historical packages

• brainflowprobes

• dots

• easyweb

• enrichedRanges

• sgejobs

• shinycsv

Non R-packages

Note: some of these GitHub repositories are currently private but will eventually become public.

LIBD

• 10xPilot_snRNAseq-human

• brain-epigenomics

• brainseq_phase2

• DLPFC_snRNAseq

• globus

• HumanPilot

• jhpce_module_config

• jhpce_mod_source

• qsva_brain

• spatialDLPFC

• SPEAQeasy

• SPEAQeasy-example

• VistoSeg

• Visium_SPG_AD

• visiumStitched_brain

• zandiHyde_bipolar_rnaseq

recount2 related

• expr_shape

• insp

• marchionni_projects

• recount-analyses

• recount-brain

• recount.bwtool

• recount-contributions

• recount-website

• recount_pandey

• recountWorkshop

• recountWorkshop2019

• recountWorkshop2020

• ryten_work

recount3 related

• recount3-docs

derfinder related

• derSoftware

• derSupplement

• libd_n36

• regionReportSupp

Team related

• bioc_team_ds

• DSgs_logs

• lcolladotorsource

• team_faces

• team_surveys

Misc

• cdsbsource

• config_jhpce

• cv

• jhu-thesis-template

• pkgs

• twitter-stats

Session info

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.5.1 (2025-06-13)
#>  os       macOS Sequoia 15.6.1
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2025-08-28
#>  pandoc   3.7.0.2 @ /opt/homebrew/bin/ (via rmarkdown)
#>  quarto   1.4.550 @ /usr/local/bin/quarto
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  BiocManager   1.30.26 2025-06-05 [1] CRAN (R 4.5.0)
#>  BiocStyle   * 2.36.0  2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  bslib         0.9.0   2025-01-30 [1] CRAN (R 4.5.0)
#>  cachem        1.1.0   2024-05-16 [1] CRAN (R 4.5.0)
#>  cli           3.6.5   2025-04-23 [1] CRAN (R 4.5.0)
#>  colorout    * 1.3-2   2025-05-09 [1] Github (jalvesaq/colorout@572ab10)
#>  digest        0.6.37  2024-08-19 [1] CRAN (R 4.5.0)
#>  evaluate      1.0.4   2025-06-18 [1] CRAN (R 4.5.0)
#>  fastmap       1.2.0   2024-05-15 [1] CRAN (R 4.5.0)
#>  htmltools     0.5.8.1 2024-04-04 [1] CRAN (R 4.5.0)
#>  jquerylib     0.1.4   2021-04-26 [1] CRAN (R 4.5.0)
#>  jsonlite      2.0.0   2025-03-27 [1] CRAN (R 4.5.0)
#>  knitr         1.50    2025-03-16 [1] CRAN (R 4.5.0)
#>  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.5.0)
#>  R6            2.6.1   2025-02-15 [1] CRAN (R 4.5.0)
#>  rlang         1.1.6   2025-04-11 [1] CRAN (R 4.5.0)
#>  rmarkdown     2.29    2024-11-04 [1] CRAN (R 4.5.0)
#>  rstudioapi    0.17.1  2024-10-22 [1] CRAN (R 4.5.0)
#>  sass          0.4.10  2025-04-11 [1] CRAN (R 4.5.0)
#>  sessioninfo * 1.2.3   2025-02-05 [1] CRAN (R 4.5.0)
#>  xfun          0.52    2025-04-02 [1] CRAN (R 4.5.0)
#>  yaml          2.3.10  2024-07-26 [1] CRAN (R 4.5.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library
#>  * ── Packages attached to the search path.
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────