sessioninfo::session_info(
installed.packages()[,"Package"],
include_base = TRUE
)
## β Session info ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
## setting value
## version R Under development (unstable) (2025-03-14 r87973)
## os Ubuntu 24.04.2 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_IN.utf8
## ctype en_IN.utf8
## tz Europe/Paris
## date 2025-04-18
## pandoc 3.1.3 @ /usr/bin/ (via rmarkdown)
## quarto 1.5.55 @ /opt/quarto/bin/quarto
##
## β Packages ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
## package * version date (UTC) lib source
## abind 1.4-8 2024-09-12 [1] CRAN (R 4.6.0)
## additivityTests 1.1-4.2 2024-05-14 [1] CRAN (R 4.6.0)
## ade4 1.7-23 2025-02-14 [1] CRAN (R 4.6.0)
## affy 1.85.1 2025-01-10 [1] Bioconduc~
## affyio 1.77.3 2025-01-24 [1] Bioconduc~
## aggregation 1.0.1 2018-01-25 [1] CRAN (R 4.6.0)
## airway 1.27.0 2024-10-31 [1] Bioconduc~
## alabaster.schemas 1.7.0 2024-10-29 [1] Bioconduc~
## alphashape3d 1.3.2 2023-01-24 [1] CRAN (R 4.6.0)
## annotate 1.85.0 2024-10-29 [1] Bioconduc~
## AnnotationDbi 1.69.0 2024-10-29 [1] Bioconduc~
## AnnotationFilter 1.31.0 2024-10-29 [1] Bioconduc~
## AnnotationForge 1.49.0 2024-10-29 [1] Bioconduc~
## AnnotationHub 3.15.0 2024-10-29 [1] Bioconduc~
## AnnotationHubData 1.37.1 2025-03-11 [1] Bioconduc~
## anytime 0.3.11 2024-12-19 [1] CRAN (R 4.6.0)
## aod 1.3.3 2023-12-13 [1] CRAN (R 4.6.0)
## ape 5.8-1 2024-12-16 [1] CRAN (R 4.6.0)
## apeglm 1.29.0 2024-10-29 [1] Bioconduc~
## aplot 0.2.5 2025-02-27 [1] CRAN (R 4.6.0)
## arrayhelpers 1.1-0 2020-02-04 [1] CRAN (R 4.6.0)
## arrow 19.0.1 2025-02-26 [1] CRAN (R 4.6.0)
## ash 1.0-15 2015-09-01 [1] CRAN (R 4.6.0)
## askpass 1.2.1 2024-10-04 [1] CRAN (R 4.6.0)
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.6.0)
## assorthead 1.1.16 2025-03-06 [1] Bioconduc~
## attachment 0.4.5 2025-03-14 [1] CRAN (R 4.6.0)
## attempt 0.3.1 2020-05-03 [1] CRAN (R 4.6.0)
## available 1.1.0 2022-07-10 [1] CRAN (R 4.6.0)
## aws.s3 0.3.21 2020-04-07 [1] CRAN (R 4.6.0)
## aws.signature 0.6.0 2020-06-01 [1] CRAN (R 4.6.0)
## AzureAuth 1.3.3 2021-09-13 [1] CRAN (R 4.6.0)
## AzureGraph 1.3.4 2023-09-06 [1] CRAN (R 4.6.0)
## AzureRMR 2.4.4 2023-09-21 [1] CRAN (R 4.6.0)
## AzureStor 3.7.0 2022-05-25 [1] CRAN (R 4.6.0)
## babelgene 22.9 2022-09-29 [1] CRAN (R 4.6.0)
## backports 1.5.0 2024-05-23 [1] CRAN (R 4.6.0)
## badger 0.2.4 2024-06-08 [1] CRAN (R 4.6.0)
## base * 4.6.0 2025-03-15 [2] local
## base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.6.0)
## basilisk 1.19.1 2025-02-12 [1] Bioconduc~
## basilisk.utils 1.19.1 2025-02-12 [1] Bioconduc~
## batchelor 1.23.0 2024-10-29 [1] Bioconduc~
## bbmle 1.0.25.1 2023-12-09 [1] CRAN (R 4.6.0)
## bdsmatrix 1.3-7 2024-03-02 [1] CRAN (R 4.6.0)
## beachmat 2.23.6 2024-12-22 [1] Bioconduc~
## beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.6.0)
## bench 1.1.4 2025-01-16 [1] CRAN (R 4.6.0)
## BH 1.87.0-1 2024-12-17 [1] CRAN (R 4.6.0)
## bibtex 0.5.1 2023-01-26 [1] CRAN (R 4.6.0)
## biclust 2.0.3.1 2023-05-19 [1] CRAN (R 4.6.0)
## bigassertr 0.1.6 2023-01-10 [1] CRAN (R 4.6.0)
## biglm 0.9-3 2024-06-12 [1] CRAN (R 4.6.0)
## bigparallelr 0.3.2 2021-10-02 [1] CRAN (R 4.6.0)
## bigreadr 0.2.5 2022-12-06 [1] CRAN (R 4.6.0)
## bigstatsr 1.6.1 2024-09-09 [1] CRAN (R 4.6.0)
## Biobase 2.67.0 2024-10-29 [1] Bioconduc~
## BiocBaseUtils 1.9.0 2024-10-29 [1] Bioconduc~
## BiocBook 1.5.0 2024-12-20 [1] Bioconduc~
## BiocCheck 1.43.12 2025-02-21 [1] Bioconduc~
## BiocFileCache 2.15.1 2025-01-17 [1] Bioconduc~
## BiocGenerics 0.53.6 2025-01-27 [1] Bioconductor 3.21 (R 4.6.0)
## BiocIO 1.17.1 2024-11-21 [1] Bioconduc~
## BiocManager 1.30.25 2024-08-28 [1] CRAN (R 4.6.0)
## BiocNeighbors 2.1.3 2025-03-05 [1] Bioconduc~
## BiocParallel 1.41.2 2025-02-19 [1] Bioconduc~
## BiocPkgTools 1.25.8 2025-03-06 [1] Bioconduc~
## BiocSingular 1.23.0 2024-10-29 [1] Bioconduc~
## BiocStyle 2.35.0 2024-10-29 [1] Bioconduc~
## biocthis 1.17.0 2024-10-29 [1] Bioconduc~
## BiocVersion 3.21.1 2024-10-29 [1] Bioconductor 3.21 (R 4.6.0)
## biocViews 1.75.0 2024-10-29 [1] Bioconduc~
## biomaRt 2.63.1 2025-01-29 [1] Bioconduc~
## biomartr 1.0.7 2023-12-02 [1] CRAN (R 4.6.0)
## biomformat 1.35.0 2024-10-29 [1] Bioconduc~
## Biostrings 2.75.4 2025-02-21 [1] Bioconduc~
## biovizBase 1.55.0 2024-10-29 [1] Bioconduc~
## bit 4.6.0 2025-03-06 [1] CRAN (R 4.6.0)
## bit64 4.6.0-1 2025-01-16 [1] CRAN (R 4.6.0)
## bitops 1.0-9 2024-10-03 [1] CRAN (R 4.6.0)
## blme 1.0-6 2024-09-07 [1] CRAN (R 4.6.0)
## blob 1.2.4 2023-03-17 [1] CRAN (R 4.6.0)
## bluster 1.17.0 2024-10-29 [1] Bioconduc~
## bookdown 0.42 2025-01-07 [1] CRAN (R 4.6.0)
## boot 1.3-31 2024-08-28 [2] CRAN (R 4.6.0)
## bootstrap 2019.6 2019-06-17 [1] CRAN (R 4.6.0)
## brew 1.0-10 2023-12-16 [1] CRAN (R 4.6.0)
## brio 1.1.5 2024-04-24 [1] CRAN (R 4.6.0)
## broom 1.0.7 2024-09-26 [1] CRAN (R 4.6.0)
## broom.helpers 1.20.0 2025-03-06 [1] CRAN (R 4.6.0)
## BrowserViz 2.29.0 2024-10-29 [1] Bioconduc~
## bs4Dash 2.3.4 2024-09-03 [1] CRAN (R 4.6.0)
## BSgenome 1.75.1 2025-01-22 [1] Bioconduc~
## BSgenome.Celegans.UCSC.ce10 1.4.0 2025-03-15 [1] Bioconductor
## BSgenome.Celegans.UCSC.ce11 1.4.2 2025-03-15 [1] Bioconductor
## BSgenome.Celegans.UCSC.ce2 1.4.0 2025-03-15 [1] Bioconductor
## BSgenome.Ggallus.UCSC.galGal5 1.4.2 2025-03-15 [1] Bioconductor
## BSgenome.Hsapiens.UCSC.hg18 1.3.1000 2025-03-15 [1] Bioconductor
## BSgenome.Hsapiens.UCSC.hg38 1.4.5 2025-03-15 [1] Bioconductor
## BSgenome.Mmusculus.UCSC.mm10 1.4.3 2025-03-15 [1] Bioconductor
## BSgenome.Scerevisiae.UCSC.sacCer3 1.4.0 2025-03-15 [1] Bioconductor
## bsicons 0.1.2 2023-11-04 [1] CRAN (R 4.6.0)
## bslib 0.9.0 2025-01-30 [1] CRAN (R 4.6.0)
## bumphunter 1.49.0 2024-10-29 [1] Bioconduc~
## BumpyMatrix 1.15.0 2024-10-29 [1] Bioconduc~
## ca 0.71.1 2020-01-24 [1] CRAN (R 4.6.0)
## cachem 1.1.0 2024-05-16 [1] CRAN (R 4.6.0)
## Cairo 1.6-2 2023-11-28 [1] CRAN (R 4.6.0)
## calibrate 1.7.7 2020-06-19 [1] CRAN (R 4.6.0)
## callr 3.7.6 2024-03-25 [1] CRAN (R 4.6.0)
## car 3.1-3 2024-09-27 [1] CRAN (R 4.6.0)
## carData 3.0-5 2022-01-06 [1] CRAN (R 4.6.0)
## cards 0.5.1 2025-03-01 [1] CRAN (R 4.6.0)
## caret 7.0-1 2024-12-10 [1] CRAN (R 4.6.0)
## caretEnsemble 4.0.1 2024-09-12 [1] CRAN (R 4.6.0)
## caTools 1.18.3 2024-09-04 [1] CRAN (R 4.6.0)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.6.0)
## CGHbase 1.67.0 2024-10-29 [1] Bioconduc~
## CGHcall 2.69.0 2024-10-29 [1] Bioconduc~
## checkmate 2.3.2 2024-07-29 [1] CRAN (R 4.6.0)
## chemometrics 1.4.4 2023-08-25 [1] CRAN (R 4.6.0)
## ChIPpeakAnno 3.41.1 2025-01-03 [1] Bioconduc~
## ChIPseeker 1.43.0 2024-10-29 [1] Bioconduc~
## cicerone 1.0.4 2021-01-10 [1] CRAN (R 4.6.0)
## circlize 0.4.16 2024-02-20 [1] CRAN (R 4.6.0)
## class 7.3-23 2025-01-01 [2] CRAN (R 4.6.0)
## classInt 0.4-11 2025-01-08 [1] CRAN (R 4.6.0)
## cli 3.6.4 2025-02-13 [1] CRAN (R 4.6.0)
## clipr 0.8.0 2022-02-22 [1] CRAN (R 4.6.0)
## clisymbols 1.2.0 2017-05-21 [1] CRAN (R 4.6.0)
## clock 0.7.2 2025-01-21 [1] CRAN (R 4.6.0)
## clue 0.3-66 2024-11-13 [1] CRAN (R 4.6.0)
## cluster 2.1.8.1 2025-03-12 [2] CRAN (R 4.6.0)
## clusterProfiler 4.15.1 2024-11-29 [1] Bioconduc~
## cmdfun 1.0.2 2020-10-10 [1] CRAN (R 4.6.0)
## cobiclust 0.1.2 2024-02-16 [1] CRAN (R 4.6.0)
## coda 0.19-4.1 2024-01-31 [1] CRAN (R 4.6.0)
## CodeDepends 0.6.6 2024-04-07 [1] CRAN (R 4.6.0)
## codetools 0.2-20 2024-03-31 [2] CRAN (R 4.6.0)
## coin 1.4-3 2023-09-27 [1] CRAN (R 4.6.0)
## collections 0.3.7 2023-01-05 [1] CRAN (R 4.6.0)
## colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.6.0)
## colourpicker 1.3.0 2023-08-21 [1] CRAN (R 4.6.0)
## colourvalues 0.3.9 2023-04-11 [1] CRAN (R 4.6.0)
## commonmark 1.9.5 2025-03-17 [1] CRAN (R 4.6.0)
## compiler 4.6.0 2025-03-15 [2] local
## ComplexHeatmap 2.23.0 2024-10-29 [1] Bioconduc~
## CompQuadForm 1.4.3 2017-04-12 [1] CRAN (R 4.6.0)
## config 0.3.2 2023-08-30 [1] CRAN (R 4.6.0)
## conflicted 1.2.0 2023-02-01 [1] CRAN (R 4.6.0)
## corpcor 1.6.10 2021-09-16 [1] CRAN (R 4.6.0)
## corrplot 0.95 2024-10-14 [1] CRAN (R 4.6.0)
## corrr 0.4.4 2022-08-16 [1] CRAN (R 4.6.0)
## countrycode 1.6.0 2024-03-22 [1] CRAN (R 4.6.0)
## covr 3.6.4 2023-11-09 [1] CRAN (R 4.6.0)
## cowplot 1.1.3 2024-01-22 [1] CRAN (R 4.6.0)
## cplm 0.7-12.1 2024-09-21 [1] CRAN (R 4.6.0)
## cpp11 0.5.2 2025-03-03 [1] CRAN (R 4.6.0)
## cranlogs 2.1.1 2019-04-29 [1] CRAN (R 4.6.0)
## crayon 1.5.3 2024-06-20 [1] CRAN (R 4.6.0)
## credentials 2.0.2 2024-10-04 [1] CRAN (R 4.6.0)
## crisprBase 1.11.0 2024-10-29 [1] Bioconduc~
## crisprBowtie 1.11.0 2024-10-29 [1] Bioconduc~
## crisprDesign 1.9.0 2024-10-29 [1] Bioconduc~
## crisprScore 1.11.0 2024-10-29 [1] Bioconduc~
## crisprScoreData 1.11.0 2024-11-05 [1] Bioconduc~
## crisprVerse 1.9.0 2024-10-30 [1] Bioconduc~
## crisprViz 1.9.0 2024-10-29 [1] Bioconduc~
## crosstalk 1.2.1 2023-11-23 [1] CRAN (R 4.6.0)
## crul 1.5.0 2024-07-19 [1] CRAN (R 4.6.0)
## csaw 1.41.2 2025-01-29 [1] Bioconduc~
## curatedMetagenomicData 3.15.0 2024-11-05 [1] Bioconduc~
## curatedTCGAData 1.29.2 2024-11-14 [1] Bioconduc~
## curl 6.2.1 2025-02-19 [1] CRAN (R 4.6.0)
## CVXR 1.0-15 2024-11-07 [1] CRAN (R 4.6.0)
## cyclocomp 1.1.1 2023-08-30 [1] CRAN (R 4.6.0)
## data.table 1.17.0 2025-02-22 [1] CRAN (R 4.6.0)
## datasets * 4.6.0 2025-03-15 [2] local
## DBI 1.2.3 2024-06-02 [1] CRAN (R 4.6.0)
## dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.6.0)
## dbscan 1.2.2 2025-01-26 [1] CRAN (R 4.6.0)
## dearseq 1.19.0 2024-10-29 [1] Bioconduc~
## DECIPHER 3.3.4 2025-03-11 [1] Bioconduc~
## decontam 1.27.0 2024-10-29 [1] Bioconduc~
## decoupleR 2.13.0 2024-10-29 [1] Bioconduc~
## DelayedArray 0.33.6 2025-02-14 [1] Bioconduc~
## DelayedMatrixStats 1.29.1 2025-01-09 [1] Bioconduc~
## deldir 2.0-4 2024-02-28 [1] CRAN (R 4.6.0)
## dendextend 1.19.0 2024-11-15 [1] CRAN (R 4.6.0)
## densvis 1.17.0 2024-10-29 [1] Bioconduc~
## DEoptimR 1.1-3-1 2024-11-23 [1] CRAN (R 4.6.0)
## depmixS4 1.5-0 2021-05-12 [1] CRAN (R 4.6.0)
## derfinder 1.41.0 2024-12-13 [1] Bioconduc~
## derfinderHelper 1.41.0 2024-12-13 [1] Bioconduc~
## Deriv 4.1.6 2024-09-13 [1] CRAN (R 4.6.0)
## desc 1.4.3 2023-12-10 [1] CRAN (R 4.6.0)
## DESeq2 1.47.5 2025-03-05 [1] Bioconduc~
## deSolve 1.40 2023-11-27 [1] CRAN (R 4.6.0)
## devtools 2.4.5 2022-10-11 [1] CRAN (R 4.6.0)
## DFplyr 1.1.0 2024-10-29 [1] Bioconduc~
## diagram 1.6.5 2020-09-30 [1] CRAN (R 4.6.0)
## dials 1.4.0 2025-02-13 [1] CRAN (R 4.6.0)
## DiceDesign 1.10 2023-12-07 [1] CRAN (R 4.6.0)
## dichromat 2.0-0.1 2022-05-02 [1] CRAN (R 4.6.0)
## diffHic 1.39.1 2024-12-16 [1] Bioconduc~
## diffobj 0.3.5 2021-10-05 [1] CRAN (R 4.6.0)
## digest 0.6.37 2024-08-19 [1] CRAN (R 4.6.0)
## dir.expiry 1.15.0 2024-10-29 [1] Bioconduc~
## directlabels 2024.1.21 2024-01-24 [1] CRAN (R 4.6.0)
## DirichletMultinomial 1.49.0 2024-10-29 [1] Bioconduc~
## dirmult 0.1.3-5 2022-03-21 [1] CRAN (R 4.6.0)
## distributional 0.5.0 2024-09-17 [1] CRAN (R 4.6.0)
## dlstats 0.1.7 2023-05-24 [1] CRAN (R 4.6.0)
## DNAcopy 1.81.0 2024-10-29 [1] Bioconduc~
## DNAZooData 1.7.0 2024-11-05 [1] Bioconduc~
## doBy 4.6.25 2025-01-30 [1] CRAN (R 4.6.0)
## dockerfiler 0.2.4 2024-08-23 [1] CRAN (R 4.6.0)
## docopt 0.7.1 2020-06-24 [1] CRAN (R 4.6.0)
## doFuture 1.0.2 2025-03-16 [1] CRAN (R 4.6.0)
## doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.6.0)
## doRNG 1.8.6.1 2025-01-13 [1] CRAN (R 4.6.0)
## DOSE 4.1.0 2024-10-29 [1] Bioconduc~
## dotCall64 1.2 2024-10-04 [1] CRAN (R 4.6.0)
## downlit 0.4.4 2024-06-10 [1] CRAN (R 4.6.0)
## downloader 0.4 2015-07-09 [1] CRAN (R 4.6.0)
## dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.6.0)
## dqrng 0.4.1 2024-05-28 [1] CRAN (R 4.6.0)
## DropletTestFiles 1.17.0 2024-11-05 [1] Bioconduc~
## DropletUtils 1.27.2 2024-12-18 [1] Bioconduc~
## DT 0.33 2024-04-04 [1] CRAN (R 4.6.0)
## dtplyr 1.3.1 2023-03-22 [1] CRAN (R 4.6.0)
## dygraphs 1.1.1.6 2018-07-11 [1] CRAN (R 4.6.0)
## dynamicTreeCut 1.63-1 2016-03-11 [1] CRAN (R 4.6.0)
## e1071 1.7-16 2024-09-16 [1] CRAN (R 4.6.0)
## easylift 1.5.0 2024-10-29 [1] Bioconduc~
## EBImage 4.49.0 2024-10-29 [1] Bioconduc~
## ECOSolveR 0.5.5 2023-05-15 [1] CRAN (R 4.6.0)
## edgeR 4.5.9 2025-03-11 [1] Bioconduc~
## egg 0.4.5 2019-07-13 [1] CRAN (R 4.6.0)
## ellipse 0.5.0 2023-07-20 [1] CRAN (R 4.6.0)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.6.0)
## emdbook 1.3.13 2023-07-03 [1] CRAN (R 4.6.0)
## emmeans 1.10.7 2025-01-31 [1] CRAN (R 4.6.0)
## energy 1.7-12 2024-08-24 [1] CRAN (R 4.6.0)
## EnrichedHeatmap 1.37.0 2024-10-29 [1] Bioconduc~
## enrichplot 1.27.4 2025-01-08 [1] Bioconduc~
## EnsDb.Hsapiens.v75 2.99.0 2025-03-15 [1] Bioconductor
## EnsDb.Hsapiens.v86 2.99.0 2025-03-15 [1] Bioconductor
## EnsDb.Mmusculus.v79 2.99.0 2025-03-15 [1] Bioconductor
## ensembldb 2.31.0 2024-10-29 [1] Bioconduc~
## entropy 1.3.1 2021-10-02 [1] CRAN (R 4.6.0)
## EnvStats 3.0.0 2024-08-24 [1] CRAN (R 4.6.0)
## estimability 1.5.1 2024-05-12 [1] CRAN (R 4.6.0)
## eulerr 7.0.2 2024-03-28 [1] CRAN (R 4.6.0)
## evaluate 1.0.3 2025-01-10 [1] CRAN (R 4.6.0)
## Exact 3.3 2024-07-21 [1] CRAN (R 4.6.0)
## excluderanges 0.99.8 2022-12-28 [1] Bioconductor
## ExperimentHub 2.15.0 2024-10-29 [1] Bioconduc~
## ExperimentHubData 1.33.0 2024-10-29 [1] Bioconduc~
## expm 1.0-0 2024-08-19 [1] CRAN (R 4.6.0)
## factoextra 1.0.7 2020-04-01 [1] CRAN (R 4.6.0)
## FactoMineR 2.11 2024-04-20 [1] CRAN (R 4.6.0)
## fANCOVA 0.6-1 2020-11-13 [1] CRAN (R 4.6.0)
## fansi 1.0.6 2023-12-08 [1] CRAN (R 4.6.0)
## faraway 1.0.9 2025-02-07 [1] CRAN (R 4.6.0)
## farver 2.1.2 2024-05-13 [1] CRAN (R 4.6.0)
## fastcluster 1.2.6 2024-01-12 [1] CRAN (R 4.6.0)
## fastDummies 1.7.5 2025-01-20 [1] CRAN (R 4.6.0)
## fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.6.0)
## fastmatch 1.1-6 2024-12-23 [1] CRAN (R 4.6.0)
## fauxpas 0.5.2 2023-05-03 [1] CRAN (R 4.6.0)
## fBasics 4041.97 2024-08-19 [1] CRAN (R 4.6.0)
## fda 6.2.0 2024-09-17 [1] CRAN (R 4.6.0)
## fdrtool 1.2.18 2024-08-20 [1] CRAN (R 4.6.0)
## fds 1.8 2018-10-31 [1] CRAN (R 4.6.0)
## ff 4.5.2 2025-01-13 [1] CRAN (R 4.6.0)
## fftwtools 0.9-11 2021-03-01 [1] CRAN (R 4.6.0)
## fgsea 1.33.2 2024-12-19 [1] Bioconduc~
## fido 1.1.2 2025-02-27 [1] CRAN (R 4.6.0)
## filelock 1.0.3 2023-12-11 [1] CRAN (R 4.6.0)
## fillpattern 1.0.2 2024-06-24 [1] CRAN (R 4.6.0)
## fission 1.27.0 2024-10-31 [1] Bioconduc~
## fit.models 0.64 2020-08-02 [1] CRAN (R 4.6.0)
## fitdistrplus 1.2-2 2025-01-07 [1] CRAN (R 4.6.0)
## FLAMINGOrLite 0.0.0.9000 2025-03-25 [1] local (/home/rsg/repos/FLAMINGOrLite)
## flashClust 1.01-2 2012-08-21 [1] CRAN (R 4.6.0)
## flexclust 1.5.0 2025-02-28 [1] CRAN (R 4.6.0)
## flock 0.7 2016-11-12 [1] CRAN (R 4.6.0)
## FNN 1.1.4.1 2024-09-22 [1] CRAN (R 4.6.0)
## fontawesome 0.5.3 2024-11-16 [1] CRAN (R 4.6.0)
## forcats 1.0.0 2023-01-29 [1] CRAN (R 4.6.0)
## foreach 1.5.2 2022-02-02 [1] CRAN (R 4.6.0)
## foreign 0.8-88 2025-01-12 [2] CRAN (R 4.6.0)
## formatR 1.14 2023-01-17 [1] CRAN (R 4.6.0)
## Formula 1.2-5 2023-02-24 [1] CRAN (R 4.6.0)
## fourDNData 1.7.0 2024-11-05 [1] Bioconduc~
## fresh 0.2.1 2024-06-26 [1] CRAN (R 4.6.0)
## fs 1.6.5 2024-10-30 [1] CRAN (R 4.6.0)
## fst 0.9.8 2022-02-08 [1] CRAN (R 4.6.0)
## fstcore 0.10.0 2025-02-10 [1] CRAN (R 4.6.0)
## furrr 0.3.1 2022-08-15 [1] CRAN (R 4.6.0)
## futile.logger 1.4.3 2016-07-10 [1] CRAN (R 4.6.0)
## futile.options 1.0.1 2018-04-20 [1] CRAN (R 4.6.0)
## future 1.34.0 2024-07-29 [1] CRAN (R 4.6.0)
## future.apply 1.11.3 2024-10-27 [1] CRAN (R 4.6.0)
## gargle 1.5.2 2023-07-20 [1] CRAN (R 4.6.0)
## gclus 1.3.2 2019-01-07 [1] CRAN (R 4.6.0)
## genefilter 1.89.0 2024-10-29 [1] Bioconduc~
## generics 0.1.3 2022-07-05 [1] CRAN (R 4.6.0)
## GenomeInfoDb 1.43.4 2025-01-24 [1] Bioconduc~
## GenomeInfoDbData 1.2.14 2025-03-15 [1] Bioconductor
## GenomicAlignments 1.43.0 2024-10-29 [1] Bioconduc~
## GenomicFeatures 1.59.1 2024-11-07 [1] Bioconduc~
## GenomicFiles 1.43.0 2024-10-29 [1] Bioconduc~
## GenomicInteractions 1.41.0 2024-10-29 [1] Bioconduc~
## GenomicRanges 1.59.1 2024-11-15 [1] Bioconduc~
## GenSA 1.1.14.1 2024-09-21 [1] CRAN (R 4.6.0)
## geometry 0.5.2 2025-02-08 [1] CRAN (R 4.6.0)
## GEOquery 2.75.0 2024-10-29 [1] Bioconduc~
## gert 2.1.4 2024-10-14 [1] CRAN (R 4.6.0)
## getopt 1.20.4 2023-10-01 [1] CRAN (R 4.6.0)
## GetoptLong 1.0.5 2020-12-15 [1] CRAN (R 4.6.0)
## ggalluvial 0.12.5 2023-02-22 [1] CRAN (R 4.6.0)
## GGally 2.2.1 2024-02-14 [1] CRAN (R 4.6.0)
## ggbeeswarm 0.7.2 2023-04-29 [1] CRAN (R 4.6.0)
## ggbio 1.55.0 2024-10-29 [1] Bioconduc~
## ggdendro 0.2.0 2024-02-23 [1] CRAN (R 4.6.0)
## ggdist 3.3.2 2024-03-05 [1] CRAN (R 4.6.0)
## ggExtra 0.10.1 2023-08-21 [1] CRAN (R 4.6.0)
## ggforce 0.4.2 2024-02-19 [1] CRAN (R 4.6.0)
## ggfortify 0.4.17 2024-04-17 [1] CRAN (R 4.6.0)
## ggfun 0.1.8 2024-12-03 [1] CRAN (R 4.6.0)
## gghalves 0.1.4 2022-11-20 [1] CRAN (R 4.6.0)
## ggimage 0.3.3 2023-06-19 [1] CRAN (R 4.6.0)
## ggnewscale 0.5.1 2025-02-24 [1] CRAN (R 4.6.0)
## ggplot2 3.5.1 2024-04-23 [1] CRAN (R 4.6.0)
## ggplotify 0.1.2 2023-08-09 [1] CRAN (R 4.6.0)
## ggpp 0.5.8-1 2024-07-01 [1] CRAN (R 4.6.0)
## ggpubr 0.6.0 2023-02-10 [1] CRAN (R 4.6.0)
## ggrain 0.0.4 2024-01-23 [1] CRAN (R 4.6.0)
## ggraph 2.2.1 2024-03-07 [1] CRAN (R 4.6.0)
## ggrastr 1.0.2 2023-06-01 [1] CRAN (R 4.6.0)
## ggrepel 0.9.6 2024-09-07 [1] CRAN (R 4.6.0)
## ggridges 0.5.6 2024-01-23 [1] CRAN (R 4.6.0)
## ggsci 3.2.0 2024-06-18 [1] CRAN (R 4.6.0)
## ggseqlogo 0.2 2024-02-09 [1] CRAN (R 4.6.0)
## ggsignif 0.6.4 2022-10-13 [1] CRAN (R 4.6.0)
## ggstar 1.0.4 2022-11-08 [1] CRAN (R 4.6.0)
## ggstats 0.9.0 2025-03-10 [1] CRAN (R 4.6.0)
## ggtangle 0.0.6 2024-12-18 [1] CRAN (R 4.6.0)
## ggtext 0.1.2 2022-09-16 [1] CRAN (R 4.6.0)
## ggtree 3.15.0 2024-10-29 [1] Bioconduc~
## ggtreeExtra 1.17.0 2024-10-29 [1] Bioconduc~
## gh 1.4.1 2024-03-28 [1] CRAN (R 4.6.0)
## gitcreds 0.1.2 2022-09-08 [1] CRAN (R 4.6.0)
## gld 2.6.7 2025-01-17 [1] CRAN (R 4.6.0)
## glmmTMB 1.1.10 2024-09-26 [1] CRAN (R 4.6.0)
## glmnet 4.1-8 2023-08-22 [1] CRAN (R 4.6.0)
## GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.6.0)
## globals 0.16.3 2024-03-08 [1] CRAN (R 4.6.0)
## glue 1.8.0 2024-09-30 [1] CRAN (R 4.6.0)
## gmailr 2.0.0 2023-06-30 [1] CRAN (R 4.6.0)
## gmp 0.7-5 2024-08-23 [1] CRAN (R 4.6.0)
## GO.db 3.21.0 2025-03-15 [1] Bioconductor
## goftest 1.2-3 2021-10-07 [1] CRAN (R 4.6.0)
## golem 0.5.1 2024-08-27 [1] CRAN (R 4.6.0)
## googledrive 2.1.1 2023-06-11 [1] CRAN (R 4.6.0)
## googlesheets4 1.1.1 2023-06-11 [1] CRAN (R 4.6.0)
## googleVis 0.7.3 2024-05-25 [1] CRAN (R 4.6.0)
## GOSemSim 2.33.0 2024-10-29 [1] Bioconduc~
## GOTHiC 1.43.0 2024-10-29 [1] Bioconduc~
## gower 1.0.2 2024-12-17 [1] CRAN (R 4.6.0)
## GPfit 1.0-8 2019-02-08 [1] CRAN (R 4.6.0)
## gplots 3.2.0 2024-10-05 [1] CRAN (R 4.6.0)
## gprofiler2 0.2.3 2024-02-23 [1] CRAN (R 4.6.0)
## graph 1.85.1 2024-12-31 [1] Bioconduc~
## graphics * 4.6.0 2025-03-15 [2] local
## graphlayouts 1.2.2 2025-01-23 [1] CRAN (R 4.6.0)
## grDevices * 4.6.0 2025-03-15 [2] local
## grid 4.6.0 2025-03-15 [2] local
## gridBase 0.4-7 2014-02-24 [1] CRAN (R 4.6.0)
## gridExtra 2.3 2017-09-09 [1] CRAN (R 4.6.0)
## gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.6.0)
## gridtext 0.1.5 2022-09-16 [1] CRAN (R 4.6.0)
## GSEABase 1.69.1 2025-02-10 [1] Bioconduc~
## gsignal 0.3-7 2024-09-11 [1] CRAN (R 4.6.0)
## gsl 2.1-8 2023-01-24 [1] CRAN (R 4.6.0)
## gson 0.1.0 2023-03-07 [1] CRAN (R 4.6.0)
## gss 2.2-8 2024-10-11 [1] CRAN (R 4.6.0)
## GSVA 2.1.8 2025-03-12 [1] Bioconduc~
## gtable 0.3.6 2024-10-25 [1] CRAN (R 4.6.0)
## gtools 3.9.5 2023-11-20 [1] CRAN (R 4.6.0)
## gtrellis 1.39.0 2024-10-29 [1] Bioconduc~
## GUniFrac 1.8 2023-09-14 [1] CRAN (R 4.6.0)
## Gviz 1.51.0 2024-10-29 [1] Bioconduc~
## gypsum 1.3.0 2024-10-29 [1] Bioconduc~
## h5mread 0.99.4 2025-01-22 [1] Bioconduc~
## hardhat 1.4.1 2025-01-31 [1] CRAN (R 4.6.0)
## hash 2.2.6.3 2023-08-19 [1] CRAN (R 4.6.0)
## haven 2.5.4 2023-11-30 [1] CRAN (R 4.6.0)
## HCAData 1.23.1 2024-12-24 [1] Bioconduc~
## HDF5Array 1.35.15 2025-02-19 [1] Bioconduc~
## hdf5r 1.3.12 2025-01-20 [1] CRAN (R 4.6.0)
## HDO.db 1.0.0 2025-03-15 [1] Bioconductor
## hdrcde 3.4 2021-01-18 [1] CRAN (R 4.6.0)
## here 1.0.1 2020-12-13 [1] CRAN (R 4.6.0)
## HiCcompare 1.29.0 2024-10-29 [1] Bioconduc~
## HiCDataLymphoblast 1.43.0 2024-11-05 [1] Bioconduc~
## HiCDOC 1.9.2 2024-12-12 [1] Bioconduc~
## HiCExperiment 1.7.0 2024-10-29 [1] Bioconduc~
## HiContacts 1.9.0 2024-10-29 [1] Bioconduc~
## HiContactsData 1.9.0 2024-11-05 [1] Bioconduc~
## HiCool 1.7.1 2025-03-18 [1] local (/home/rsg/repos/HiCool)
## highr 0.11 2024-05-26 [1] CRAN (R 4.6.0)
## Hmisc 5.2-3 2025-03-16 [1] CRAN (R 4.6.0)
## hms 1.1.3 2023-03-21 [1] CRAN (R 4.6.0)
## htmlTable 2.4.3 2024-07-21 [1] CRAN (R 4.6.0)
## htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.6.0)
## htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.6.0)
## httpcode 0.3.0 2020-04-10 [1] CRAN (R 4.6.0)
## httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.6.0)
## httr 1.4.7 2023-08-15 [1] CRAN (R 4.6.0)
## httr2 1.1.1 2025-03-08 [1] CRAN (R 4.6.0)
## hues 0.2.0 2019-12-01 [1] CRAN (R 4.6.0)
## hunspell 3.0.5 2024-10-04 [1] CRAN (R 4.6.0)
## hwriter 1.3.2.1 2022-04-08 [1] CRAN (R 4.6.0)
## ica 1.0-3 2022-07-08 [1] CRAN (R 4.6.0)
## ids 1.0.1 2017-05-31 [1] CRAN (R 4.6.0)
## igraph 2.1.4 2025-01-23 [1] CRAN (R 4.6.0)
## igvR 1.27.0 2024-10-29 [1] Bioconduc~
## impute 1.81.0 2024-10-29 [1] Bioconduc~
## ini 0.3.1 2018-05-20 [1] CRAN (R 4.6.0)
## inline 0.3.21 2025-01-09 [1] CRAN (R 4.6.0)
## InteractionSet 1.35.0 2024-10-29 [1] Bioconduc~
## interactiveDisplayBase 1.45.0 2024-10-29 [1] Bioconduc~
## interp 1.1-6 2024-01-26 [1] CRAN (R 4.6.0)
## ipred 0.9-15 2024-07-18 [1] CRAN (R 4.6.0)
## IRanges 2.41.3 2025-02-12 [1] Bioconduc~
## irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.6.0)
## isoband 0.2.7 2022-12-20 [1] CRAN (R 4.6.0)
## iterators 1.0.14 2022-02-05 [1] CRAN (R 4.6.0)
## janeaustenr 1.0.0 2022-08-26 [1] CRAN (R 4.6.0)
## JASPAR2020 0.99.10 2025-03-15 [1] Bioconductor
## JASPAR2022 0.99.8 2024-02-28 [1] Bioconduc~
## jmuOutlier 2.2 2019-08-05 [1] CRAN (R 4.6.0)
## jose 1.2.1 2024-10-04 [1] CRAN (R 4.6.0)
## jpeg 0.1-10 2022-11-29 [1] CRAN (R 4.6.0)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.6.0)
## jsonlite 1.9.1 2025-03-03 [1] CRAN (R 4.6.0)
## jsonvalidate 1.5.0 2025-02-07 [1] CRAN (R 4.6.0)
## kableExtra 1.4.0 2024-01-24 [1] CRAN (R 4.6.0)
## KEGGREST 1.47.0 2024-10-29 [1] Bioconduc~
## kernlab 0.9-33 2024-08-13 [1] CRAN (R 4.6.0)
## KernSmooth 2.23-26 2025-01-01 [2] CRAN (R 4.6.0)
## knitr 1.50 2025-03-16 [1] CRAN (R 4.6.0)
## ks 1.14.3 2024-09-20 [1] CRAN (R 4.6.0)
## labeling 0.4.3 2023-08-29 [1] CRAN (R 4.6.0)
## labelled 2.14.0 2025-01-08 [1] CRAN (R 4.6.0)
## lambda.r 1.2.4 2019-09-18 [1] CRAN (R 4.6.0)
## languageserver 0.3.16 2023-08-18 [1] CRAN (R 4.6.0)
## lars 1.3 2022-04-13 [1] CRAN (R 4.6.0)
## later 1.4.1 2024-11-27 [1] CRAN (R 4.6.0)
## lattice 0.22-6 2024-03-20 [2] CRAN (R 4.6.0)
## latticeExtra 0.6-30 2022-07-04 [1] CRAN (R 4.6.0)
## lava 1.8.1 2025-01-12 [1] CRAN (R 4.6.0)
## lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.6.0)
## leaflet 2.2.2 2024-03-26 [1] CRAN (R 4.6.0)
## leaflet.providers 2.0.0 2023-10-17 [1] CRAN (R 4.6.0)
## leaps 3.2 2024-06-10 [1] CRAN (R 4.6.0)
## leiden 0.4.3.1 2023-11-17 [1] CRAN (R 4.6.0)
## leidenbase 0.1.32 2025-02-06 [1] CRAN (R 4.6.0)
## lemon 0.5.0 2024-11-10 [1] CRAN (R 4.6.0)
## lhs 1.2.0 2024-06-30 [1] CRAN (R 4.6.0)
## libcoin 1.0-10 2023-09-27 [1] CRAN (R 4.6.0)
## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.6.0)
## limma 3.63.9 2025-03-11 [1] Bioconduc~
## LimROTS 0.99.12 2024-12-20 [1] Bioconduc~
## linprog 0.9-4 2022-03-09 [1] CRAN (R 4.6.0)
## lintr 3.2.0 2025-02-12 [1] CRAN (R 4.6.0)
## listenv 0.9.1 2024-01-29 [1] CRAN (R 4.6.0)
## littler 0.3.20 2024-03-23 [1] CRAN (R 4.6.0)
## lme4 1.1-36 2025-01-11 [1] CRAN (R 4.6.0)
## lmerTest 3.1-3 2020-10-23 [1] CRAN (R 4.6.0)
## lmom 3.2 2024-09-30 [1] CRAN (R 4.6.0)
## lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.6.0)
## lobstr 1.1.2 2022-06-22 [1] CRAN (R 4.6.0)
## locfit 1.5-9.12 2025-03-05 [1] CRAN (R 4.6.0)
## logging 0.10-108 2019-07-14 [1] CRAN (R 4.6.0)
## LoomExperiment 1.25.0 2024-10-29 [1] Bioconduc~
## lpSolve 5.6.23 2024-12-14 [1] CRAN (R 4.6.0)
## lubridate 1.9.4 2024-12-08 [1] CRAN (R 4.6.0)
## macrophage 1.23.0 2024-10-31 [1] Bioconduc~
## magic 1.6-1 2022-11-16 [1] CRAN (R 4.6.0)
## magick 2.8.5 2024-09-20 [1] CRAN (R 4.6.0)
## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.6.0)
## mailR 0.8 2021-12-03 [1] CRAN (R 4.6.0)
## MALDIquant 1.22.3 2024-08-19 [1] CRAN (R 4.6.0)
## maps 3.4.2.1 2024-11-10 [1] CRAN (R 4.6.0)
## mariner 1.7.0 2024-10-29 [1] Bioconduc~
## markdown 1.13 2024-06-04 [1] CRAN (R 4.6.0)
## marray 1.85.0 2024-10-29 [1] Bioconduc~
## MASS 7.3-65 2025-02-28 [2] CRAN (R 4.6.0)
## MAST 1.33.0 2024-10-29 [1] Bioconduc~
## Matrix 1.7-3 2025-03-11 [2] CRAN (R 4.6.0)
## MatrixGenerics 1.19.1 2025-01-09 [1] Bioconduc~
## MatrixModels 0.5-3 2023-11-06 [1] CRAN (R 4.6.0)
## matrixStats 1.5.0 2025-01-07 [1] CRAN (R 4.6.0)
## mclust 6.1.1 2024-04-29 [1] CRAN (R 4.6.0)
## megadepth 1.17.0 2024-10-29 [1] Bioconduc~
## memes 1.15.0 2024-10-29 [1] Bioconduc~
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.6.0)
## MetaboCoreUtils 1.15.0 2024-10-29 [1] Bioconduc~
## metagene2 1.23.0 2024-10-29 [1] Bioconduc~
## metapod 1.15.0 2024-10-29 [1] Bioconduc~
## methods * 4.6.0 2025-03-15 [2] local
## metrica 2.1.0 2024-06-30 [1] CRAN (R 4.6.0)
## mgcv 1.9-1 2023-12-21 [2] CRAN (R 4.6.0)
## MGLM 0.2.1 2022-04-13 [1] CRAN (R 4.6.0)
## mia 1.15.25 2025-02-27 [1] Bioconduc~
## miaViz 1.15.9 2025-02-28 [1] Bioconduc~
## microbenchmark 1.5.0 2024-09-04 [1] CRAN (R 4.6.0)
## microbiomeDataSets 1.15.0 2024-11-05 [1] Bioconduc~
## MicrobiomeStat 1.2 2024-04-01 [1] CRAN (R 4.6.0)
## MicrobiotaProcess 1.19.0 2024-10-29 [1] Bioconduc~
## mime 0.13 2025-03-17 [1] CRAN (R 4.6.0)
## minerva 1.5.10 2021-06-17 [1] CRAN (R 4.6.0)
## miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.6.0)
## minqa 1.2.8 2024-08-17 [1] CRAN (R 4.6.0)
## misc3d 0.9-1 2021-10-07 [1] CRAN (R 4.6.0)
## mitools 2.4 2019-04-26 [1] CRAN (R 4.6.0)
## mixOmics 6.31.4 2025-01-13 [1] Bioconduc~
## MLmetrics 1.1.3 2024-04-13 [1] CRAN (R 4.6.0)
## modeest 2.4.0 2019-11-18 [1] CRAN (R 4.6.0)
## modelenv 0.2.0 2024-10-14 [1] CRAN (R 4.6.0)
## ModelMetrics 1.2.2.2 2020-03-17 [1] CRAN (R 4.6.0)
## modelr 0.1.11 2023-03-22 [1] CRAN (R 4.6.0)
## modeltools 0.2-23 2020-03-05 [1] CRAN (R 4.6.0)
## MOFA2 1.17.0 2024-10-29 [1] Bioconduc~
## monaLisa 1.13.2 2025-01-20 [1] Bioconduc~
## MotifDb 1.49.3 2025-03-13 [1] Bioconduc~
## motifmatchr 1.29.0 2024-10-29 [1] Bioconduc~
## msa 1.39.2 2025-02-14 [1] Bioconduc~
## MsBackendMetaboLights 1.1.0 2024-10-29 [1] Bioconduc~
## MsCoreUtils 1.19.1 2025-03-12 [1] Bioconduc~
## msdata 0.47.0 2024-10-31 [1] Bioconduc~
## msigdbr 10.0.0 2025-03-12 [1] CRAN (R 4.6.0)
## msmsEDA 1.45.0 2024-10-29 [1] Bioconduc~
## msmsTests 1.45.0 2024-10-29 [1] Bioconduc~
## MSnbase 2.33.3 2025-03-05 [1] Bioconduc~
## MSnID 1.41.0 2024-10-29 [1] Bioconduc~
## multcomp 1.4-28 2025-01-29 [1] CRAN (R 4.6.0)
## multcompView 0.1-10 2024-03-08 [1] CRAN (R 4.6.0)
## MultiAssayExperiment 1.33.9 2025-01-29 [1] Bioconduc~
## multicool 1.0.1 2024-02-05 [1] CRAN (R 4.6.0)
## multiHiCcompare 1.25.0 2024-10-29 [1] Bioconduc~
## multtest 2.63.0 2024-10-29 [1] Bioconduc~
## munsell 0.5.1 2024-04-01 [1] CRAN (R 4.6.0)
## Mus.musculus 1.3.1 2025-03-15 [1] Bioconductor
## muscat 1.21.0 2024-11-13 [1] Bioconduc~
## mvtnorm 1.3-3 2025-01-10 [1] CRAN (R 4.6.0)
## mzID 1.45.0 2024-10-29 [1] Bioconduc~
## mzR 2.41.4 2025-02-12 [1] Bioconduc~
## NADA 1.6-1.1 2020-03-22 [1] CRAN (R 4.6.0)
## NbClust 3.0.1 2022-05-02 [1] CRAN (R 4.6.0)
## ncdf4 1.23 2024-08-17 [1] CRAN (R 4.6.0)
## networkD3 0.4 2017-03-18 [1] CRAN (R 4.6.0)
## nlme 3.1-167 2025-01-27 [2] CRAN (R 4.6.0)
## nloptr 2.2.1 2025-03-17 [1] CRAN (R 4.6.0)
## nnet 7.3-20 2025-01-01 [2] CRAN (R 4.6.0)
## NOISeq 2.51.0 2024-10-29 [1] Bioconduc~
## nortest 1.0-4 2015-07-30 [1] CRAN (R 4.6.0)
## nucleR 2.39.0 2024-10-29 [1] Bioconduc~
## nullranges 1.13.0 2024-10-29 [1] Bioconduc~
## numbers 0.8-5 2022-11-23 [1] CRAN (R 4.6.0)
## numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.6.0)
## oct4 1.23.0 2024-10-31 [1] Bioconduc~
## OHCA 1.3.0 2024-11-11 [1] Bioconduc~
## ontologyIndex 2.12 2024-02-27 [1] CRAN (R 4.6.0)
## ontologyPlot 1.7 2024-02-20 [1] CRAN (R 4.6.0)
## ontoProc 2.1.7 2025-03-13 [1] Bioconduc~
## openssl 2.3.2 2025-02-03 [1] CRAN (R 4.6.0)
## optparse 1.7.5 2024-04-16 [1] CRAN (R 4.6.0)
## ORFik 1.27.3 2025-02-17 [1] Bioconduc~
## org.Hs.eg.db 3.21.0 2025-03-15 [1] Bioconductor
## org.Mm.eg.db 3.21.0 2025-03-15 [1] Bioconductor
## OrganismDbi 1.49.0 2024-10-29 [1] Bioconduc~
## Orthology.eg.db 3.21.0 2025-03-15 [1] Bioconductor
## osqp 0.6.3.3 2024-06-08 [1] CRAN (R 4.6.0)
## packrat 0.9.2 2023-09-05 [1] CRAN (R 4.6.0)
## paintmap 1.0 2016-08-31 [1] CRAN (R 4.6.0)
## pak 0.8.0.1 2025-01-16 [1] CRAN (R 4.6.0)
## palmerpenguins 0.1.1 2022-08-15 [1] CRAN (R 4.6.0)
## parallel 4.6.0 2025-03-15 [2] local
## parallelly 1.42.0 2025-01-30 [1] CRAN (R 4.6.0)
## parathyroidSE 1.45.1 2024-12-12 [1] Bioconduc~
## parsnip 1.3.1 2025-03-12 [1] CRAN (R 4.6.0)
## patchwork 1.3.0 2024-09-16 [1] CRAN (R 4.6.0)
## paws.common 0.8.2 2025-03-05 [1] CRAN (R 4.6.0)
## paws.storage 0.9.0 2025-03-14 [1] CRAN (R 4.6.0)
## pbapply 1.7-2 2023-06-27 [1] CRAN (R 4.6.0)
## pbkrtest 0.5.3 2024-06-26 [1] CRAN (R 4.6.0)
## pcaMethods 1.99.0 2024-10-29 [1] Bioconduc~
## pcaPP 2.0-5 2024-08-19 [1] CRAN (R 4.6.0)
## pdftools 3.5.0 2025-03-03 [1] CRAN (R 4.6.0)
## periodicDNA 1.17.0 2024-10-29 [1] Bioconduc~
## permute 0.9-7 2022-01-27 [1] CRAN (R 4.6.0)
## phangorn 2.12.1 2024-09-17 [1] CRAN (R 4.6.0)
## pheatmap 1.0.12 2019-01-04 [1] CRAN (R 4.6.0)
## philentropy 0.9.0 2024-11-12 [1] CRAN (R 4.6.0)
## philr 1.33.0 2024-10-29 [1] Bioconduc~
## phyloseq 1.51.0 2025-01-23 [1] Bioconduc~
## picante 1.8.2 2020-06-10 [1] CRAN (R 4.6.0)
## pillar 1.10.1 2025-01-07 [1] CRAN (R 4.6.0)
## pixmap 0.4-13 2024-05-03 [1] CRAN (R 4.6.0)
## pkgbuild 1.4.6 2025-01-16 [1] CRAN (R 4.6.0)
## pkgcache 2.2.3 2024-09-12 [1] CRAN (R 4.6.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.6.0)
## pkgdown 2.1.1 2024-09-17 [1] CRAN (R 4.6.0)
## pkgload 1.4.0 2024-06-28 [1] CRAN (R 4.6.0)
## pkgndep 1.99.3 2023-10-13 [1] CRAN (R 4.6.0)
## PKI 0.1-14 2024-06-15 [1] CRAN (R 4.6.0)
## plogr 0.2.0 2018-03-25 [1] CRAN (R 4.6.0)
## plot3D 1.4.1 2024-02-06 [1] CRAN (R 4.6.0)
## plotgardener 1.13.0 2024-10-29 [1] Bioconduc~
## plotly 4.10.4 2024-01-13 [1] CRAN (R 4.6.0)
## plotrix 3.8-4 2023-11-10 [1] CRAN (R 4.6.0)
## pls 2.8-5 2024-09-15 [1] CRAN (R 4.6.0)
## plyinteractions 1.5.0 2024-10-29 [1] Bioconduc~
## plyr 1.8.9 2023-10-02 [1] CRAN (R 4.6.0)
## plyranges 1.27.0 2024-10-29 [1] Bioconduc~
## png 0.1-8 2022-11-29 [1] CRAN (R 4.6.0)
## polyclip 1.10-7 2024-07-23 [1] CRAN (R 4.6.0)
## polylabelr 0.3.0 2024-11-19 [1] CRAN (R 4.6.0)
## polynom 1.4-1 2022-04-11 [1] CRAN (R 4.6.0)
## poorman 0.2.7 2023-10-30 [1] CRAN (R 4.6.0)
## posterior 1.6.1 2025-02-27 [1] CRAN (R 4.6.0)
## poweRlaw 1.0.0 2025-02-03 [1] CRAN (R 4.6.0)
## pracma 2.4.4 2023-11-10 [1] CRAN (R 4.6.0)
## praise 1.0.0 2015-08-11 [1] CRAN (R 4.6.0)
## preprocessCore 1.69.0 2024-10-29 [1] Bioconduc~
## prettydoc 0.4.1 2021-01-10 [1] CRAN (R 4.6.0)
## prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.6.0)
## princurve 2.1.6 2021-01-18 [1] CRAN (R 4.6.0)
## pROC 1.18.5 2023-11-01 [1] CRAN (R 4.6.0)
## processx 3.8.6 2025-02-21 [1] CRAN (R 4.6.0)
## prodlim 2024.06.25 2024-06-24 [1] CRAN (R 4.6.0)
## profmem 0.6.0 2020-12-13 [1] CRAN (R 4.6.0)
## profvis 0.4.0 2024-09-20 [1] CRAN (R 4.6.0)
## progress 1.2.3 2023-12-06 [1] CRAN (R 4.6.0)
## progressr 0.15.1 2024-11-22 [1] CRAN (R 4.6.0)
## promises 1.3.2 2024-11-28 [1] CRAN (R 4.6.0)
## ProtGenerics 1.39.2 2025-01-15 [1] Bioconduc~
## proxy 0.4-27 2022-06-09 [1] CRAN (R 4.6.0)
## ps 1.9.0 2025-02-18 [1] CRAN (R 4.6.0)
## pscl 1.5.9 2024-01-31 [1] CRAN (R 4.6.0)
## PSMatch 1.11.0 2024-10-29 [1] Bioconduc~
## purrr 1.0.4 2025-02-05 [1] CRAN (R 4.6.0)
## pwalign 1.3.2 2025-01-22 [1] Bioconduc~
## qap 0.1-2 2022-06-27 [1] CRAN (R 4.6.0)
## QDNAseq 1.43.0 2024-10-29 [1] Bioconduc~
## QFeatures 1.17.4 2025-03-04 [1] Bioconduc~
## qpdf 1.3.4 2024-10-04 [1] CRAN (R 4.6.0)
## qqman 0.1.9 2023-08-23 [1] CRAN (R 4.6.0)
## quadprog 1.5-8 2019-11-20 [1] CRAN (R 4.6.0)
## quantreg 6.1 2025-03-10 [1] CRAN (R 4.6.0)
## quarto 1.4.4 2024-07-20 [1] CRAN (R 4.6.0)
## qvalue 2.39.0 2024-10-29 [1] Bioconduc~
## R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.6.0)
## R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.6.0)
## R.oo 1.27.0 2024-11-01 [1] CRAN (R 4.6.0)
## R.utils 2.13.0 2025-02-24 [1] CRAN (R 4.6.0)
## R2HTML 2.3.4 2024-06-16 [1] CRAN (R 4.6.0)
## R453Plus1Toolbox 1.57.0 2024-10-29 [1] Bioconduc~
## R6 2.6.1 2025-02-15 [1] CRAN (R 4.6.0)
## ragg 1.3.3 2024-09-11 [1] CRAN (R 4.6.0)
## RaggedExperiment 1.31.1 2024-11-24 [1] Bioconduc~
## rainbow 3.8 2024-01-23 [1] CRAN (R 4.6.0)
## ramify 0.3.3 2016-12-17 [1] CRAN (R 4.6.0)
## randomcoloR 1.1.0.1 2019-11-24 [1] CRAN (R 4.6.0)
## randomForest 4.7-1.2 2024-09-22 [1] CRAN (R 4.6.0)
## randomNames 1.6-0.0 2024-05-04 [1] CRAN (R 4.6.0)
## RANN 2.6.2 2024-08-25 [1] CRAN (R 4.6.0)
## rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.6.0)
## rARPACK 0.11-0 2016-03-10 [1] CRAN (R 4.6.0)
## raster 3.6-31 2025-01-16 [1] CRAN (R 4.6.0)
## RBGL 1.83.0 2024-10-29 [1] Bioconduc~
## rbibutils 2.3 2024-10-04 [1] CRAN (R 4.6.0)
## rbiom 2.1.1 2025-03-10 [1] CRAN (R 4.6.0)
## Rbowtie 1.47.0 2024-10-29 [1] Bioconduc~
## rcmdcheck 1.4.0 2021-09-27 [1] CRAN (R 4.6.0)
## RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.6.0)
## Rcpp 1.0.14 2025-01-12 [1] CRAN (R 4.6.0)
## RcppAnnoy 0.0.22 2024-01-23 [1] CRAN (R 4.6.0)
## RcppArmadillo 14.4.0-1 2025-03-18 [1] CRAN (R 4.6.0)
## RcppEigen 0.3.4.0.2 2024-08-24 [1] CRAN (R 4.6.0)
## RcppGSL 0.3.13 2023-01-13 [1] CRAN (R 4.6.0)
## RcppHNSW 0.6.0 2024-02-04 [1] CRAN (R 4.6.0)
## RcppML 0.3.7 2021-09-21 [1] CRAN (R 4.6.0)
## RcppNumerical 0.6-0 2023-09-06 [1] CRAN (R 4.6.0)
## RcppParallel 5.1.10 2025-01-24 [1] CRAN (R 4.6.0)
## RcppProgress 0.4.2 2020-02-06 [1] CRAN (R 4.6.0)
## RcppRoll 0.3.1 2024-07-07 [1] CRAN (R 4.6.0)
## RcppThread 2.2.0 2025-01-07 [1] CRAN (R 4.6.0)
## RcppTOML 0.2.3 2025-03-08 [1] CRAN (R 4.6.0)
## RcppZiggurat 0.1.6 2020-10-20 [1] CRAN (R 4.6.0)
## rcrossref 1.2.0 2022-11-11 [1] CRAN (R 4.6.0)
## RCurl 1.98-1.16 2024-07-11 [1] CRAN (R 4.6.0)
## Rdpack 2.6.3 2025-03-16 [1] CRAN (R 4.6.0)
## readr 2.1.5 2024-01-10 [1] CRAN (R 4.6.0)
## readxl 1.4.5 2025-03-07 [1] CRAN (R 4.6.0)
## rebook 1.17.0 2024-10-29 [1] Bioconduc~
## recipes 1.2.0 2025-03-17 [1] CRAN (R 4.6.0)
## REDseq 1.53.0 2024-10-29 [1] Bioconduc~
## RefManageR 1.4.0 2022-09-30 [1] CRAN (R 4.6.0)
## reformulas 0.4.0 2024-11-03 [1] CRAN (R 4.6.0)
## regioneR 1.39.0 2024-10-29 [1] Bioconduc~
## registry 0.5-1 2019-03-05 [1] CRAN (R 4.6.0)
## remaCor 0.0.18 2024-02-08 [1] CRAN (R 4.6.0)
## rematch 2.0.0 2023-08-30 [1] CRAN (R 4.6.0)
## rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.6.0)
## remotes 2.5.0 2024-03-17 [1] CRAN (R 4.6.0)
## rentrez 1.2.3 2020-11-10 [1] CRAN (R 4.6.0)
## renv 1.1.3 2025-03-18 [1] CRAN (R 4.6.0)
## Repliscope 1.1.1 2022-09-13 [1] CRAN (R 4.6.0)
## reprex 2.1.1 2024-07-06 [1] CRAN (R 4.6.0)
## reshape 0.8.9 2022-04-12 [1] CRAN (R 4.6.0)
## reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.6.0)
## ResidualMatrix 1.17.0 2024-10-29 [1] Bioconduc~
## restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.6.0)
## reticulate 1.41.0.1 2025-03-09 [1] CRAN (R 4.6.0)
## revealjs 0.9 2017-03-13 [1] CRAN (R 4.6.0)
## rex 1.2.1 2021-11-26 [1] CRAN (R 4.6.0)
## Rfast 2.1.5.1 2025-03-14 [1] CRAN (R 4.6.0)
## rgl 1.3.17 2025-01-17 [1] CRAN (R 4.6.0)
## Rgraphviz 2.51.1 2025-02-25 [1] Bioconduc~
## rhdf5 2.51.2 2025-01-08 [1] Bioconduc~
## rhdf5filters 1.19.2 2025-03-05 [1] Bioconduc~
## Rhdf5lib 1.29.1 2025-02-27 [1] Bioconduc~
## RhpcBLASctl 0.23-42 2023-02-11 [1] CRAN (R 4.6.0)
## Rhtslib 3.3.2 2025-03-05 [1] Bioconduc~
## rJava 1.0-11 2024-01-26 [1] CRAN (R 4.6.0)
## rjson 0.2.23 2024-09-16 [1] CRAN (R 4.6.0)
## rjsoncons 1.3.2 2025-03-15 [1] CRAN (R 4.6.0)
## rlang 1.1.5 2025-01-17 [1] CRAN (R 4.6.0)
## rmarkdown 2.29 2024-11-04 [1] CRAN (R 4.6.0)
## rmdformats 1.0.4 2022-05-17 [1] CRAN (R 4.6.0)
## rmio 0.4.0 2022-02-17 [1] CRAN (R 4.6.0)
## Rmisc 1.5.1 2022-05-02 [1] CRAN (R 4.6.0)
## Rmpfr 1.0-0 2024-11-18 [1] CRAN (R 4.6.0)
## rmutil 1.1.10 2022-10-27 [1] CRAN (R 4.6.0)
## rngtools 1.5.2 2021-09-20 [1] CRAN (R 4.6.0)
## robust 0.7-5 2024-08-17 [1] CRAN (R 4.6.0)
## robustbase 0.99-4-1 2024-09-27 [1] CRAN (R 4.6.0)
## RobustLinearReg 1.2.0 2020-06-12 [1] CRAN (R 4.6.0)
## ROC 1.83.0 2024-10-29 [1] Bioconduc~
## ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.6.0)
## rootSolve 1.8.2.4 2023-09-21 [1] CRAN (R 4.6.0)
## rorcid 0.7.0 2021-01-20 [1] CRAN (R 4.6.0)
## roxygen2 7.3.2 2024-06-28 [1] CRAN (R 4.6.0)
## rpart 4.1.24 2025-01-07 [2] CRAN (R 4.6.0)
## rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.6.0)
## rpx 2.15.1 2025-02-09 [1] Bioconduc~
## rrcov 1.7-6 2024-08-19 [1] CRAN (R 4.6.0)
## rsample 1.2.1 2024-03-25 [1] CRAN (R 4.6.0)
## Rsamtools 2.23.1 2024-11-27 [1] Bioconduc~
## rsconnect 1.3.4 2025-01-22 [1] CRAN (R 4.6.0)
## Rsolnp 1.16 2015-12-28 [1] CRAN (R 4.6.0)
## RSpectra 0.16-2 2024-07-18 [1] CRAN (R 4.6.0)
## rspm 0.6.1 2024-10-29 [1] CRAN (R 4.6.0)
## RSQLite 2.3.9 2024-12-03 [1] CRAN (R 4.6.0)
## rstatix 0.7.2 2023-02-01 [1] CRAN (R 4.6.0)
## rstudioapi 0.17.1 2024-10-22 [1] CRAN (R 4.6.0)
## Rsubread 2.21.1 2024-11-01 [1] Bioconduc~
## rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.6.0)
## rtracklayer 1.67.1 2025-02-19 [1] Bioconduc~
## Rtsne 0.17 2023-12-07 [1] CRAN (R 4.6.0)
## RUnit 0.4.33 2024-02-22 [1] CRAN (R 4.6.0)
## rvcheck 0.2.1 2021-10-22 [1] CRAN (R 4.6.0)
## rversions 2.1.2 2022-08-31 [1] CRAN (R 4.6.0)
## rvest 1.0.4 2024-02-12 [1] CRAN (R 4.6.0)
## rworkflows 1.0.6 2025-01-23 [1] CRAN (R 4.6.0)
## s2 1.1.7 2024-07-17 [1] CRAN (R 4.6.0)
## S4Arrays 1.7.3 2025-02-09 [1] Bioconduc~
## S4Vectors 0.45.4 2025-02-11 [1] Bioconductor 3.21 (R 4.6.0)
## saferDev 1.0 2025-03-25 [1] local (/home/rsg/repos/saferDev)
## sandwich 3.1-1 2024-09-15 [1] CRAN (R 4.6.0)
## sass 0.4.9 2024-03-15 [1] CRAN (R 4.6.0)
## ScaledMatrix 1.15.0 2024-10-29 [1] Bioconduc~
## scales 1.3.0 2023-11-28 [1] CRAN (R 4.6.0)
## scater 1.35.4 2025-03-07 [1] Bioconduc~
## scattermore 1.2 2023-06-12 [1] CRAN (R 4.6.0)
## scatterpie 0.2.4 2024-08-28 [1] CRAN (R 4.6.0)
## scatterplot3d 0.3-44 2023-05-05 [1] CRAN (R 4.6.0)
## scDblFinder 1.21.1 2025-01-08 [1] Bioconduc~
## scmap 1.29.0 2024-10-29 [1] Bioconduc~
## scran 1.35.0 2024-10-29 [1] Bioconduc~
## scs 3.2.4 2023-04-11 [1] CRAN (R 4.6.0)
## sctransform 0.4.1 2023-10-19 [1] CRAN (R 4.6.0)
## scuttle 1.17.0 2024-10-29 [1] Bioconduc~
## sechm 1.15.1 2025-02-20 [1] Bioconduc~
## segmented 2.1-4 2025-02-28 [1] CRAN (R 4.6.0)
## selectr 0.4-2 2019-11-20 [1] CRAN (R 4.6.0)
## sendmailR 1.4-0 2023-01-12 [1] CRAN (R 4.6.0)
## seqinr 4.2-36 2023-12-08 [1] CRAN (R 4.6.0)
## seqLogo 1.73.0 2024-10-29 [1] Bioconduc~
## seriation 1.5.7 2024-12-05 [1] CRAN (R 4.6.0)
## servr 0.32 2024-10-04 [1] CRAN (R 4.6.0)
## sessioninfo 1.2.3 2025-02-05 [1] CRAN (R 4.6.0)
## Seurat 5.2.1 2025-01-24 [1] CRAN (R 4.6.0)
## SeuratObject 5.0.2 2024-05-08 [1] CRAN (R 4.6.0)
## sfd 0.1.0 2024-01-08 [1] CRAN (R 4.6.0)
## shadowtext 0.1.4 2024-07-18 [1] CRAN (R 4.6.0)
## shape 1.4.6.1 2024-02-23 [1] CRAN (R 4.6.0)
## shinipsum 0.1.1 2024-02-09 [1] CRAN (R 4.6.0)
## shiny 1.10.0 2024-12-14 [1] CRAN (R 4.6.0)
## shinyAce 0.4.4 2025-02-03 [1] CRAN (R 4.6.0)
## shinyalert 3.1.0 2024-04-27 [1] CRAN (R 4.6.0)
## shinydashboard 0.7.2 2021-09-30 [1] CRAN (R 4.6.0)
## shinydashboardPlus 2.0.5 2024-08-18 [1] CRAN (R 4.6.0)
## shinyFeedback 0.4.0 2021-09-23 [1] CRAN (R 4.6.0)
## shinyjs 2.1.0 2021-12-23 [1] CRAN (R 4.6.0)
## shinyTime 1.0.3 2022-08-19 [1] CRAN (R 4.6.0)
## shinytoastr 2.2.0 2023-08-30 [1] CRAN (R 4.6.0)
## shinyWidgets 0.9.0 2025-02-21 [1] CRAN (R 4.6.0)
## ShortRead 1.65.0 2024-10-29 [1] Bioconduc~
## Signac 1.14.0 2024-08-21 [1] CRAN (R 4.6.0)
## SingleCellExperiment 1.29.2 2025-03-07 [1] Bioconduc~
## SingleR 2.9.6 2025-02-16 [1] Bioconduc~
## singscore 1.27.0 2024-10-29 [1] Bioconduc~
## sitmo 2.0.2 2021-10-13 [1] CRAN (R 4.6.0)
## slam 0.1-55 2024-11-13 [1] CRAN (R 4.6.0)
## slider 0.3.2 2024-10-25 [1] CRAN (R 4.6.0)
## slingshot 2.15.0 2024-10-29 [1] Bioconduc~
## sm 2.2-6.0 2024-02-17 [1] CRAN (R 4.6.0)
## snow 0.4-4 2021-10-27 [1] CRAN (R 4.6.0)
## SnowballC 0.7.1 2023-04-25 [1] CRAN (R 4.6.0)
## snowfall 1.84-6.3 2023-11-26 [1] CRAN (R 4.6.0)
## softImpute 1.4-1 2021-05-09 [1] CRAN (R 4.6.0)
## som 0.3-5.2 2024-09-18 [1] CRAN (R 4.6.0)
## sourcetools 0.1.7-1 2023-02-01 [1] CRAN (R 4.6.0)
## sp 2.2-0 2025-02-01 [1] CRAN (R 4.6.0)
## spam 2.11-1 2025-01-20 [1] CRAN (R 4.6.0)
## Spaniel 1.21.0 2024-10-29 [1] Bioconduc~
## SpaNorm 1.1.0 2024-10-29 [1] Bioconduc~
## SparseArray 1.7.6 2025-02-19 [1] Bioconduc~
## SparseM 1.84-2 2024-07-17 [1] CRAN (R 4.6.0)
## sparseMatrixStats 1.19.0 2024-10-29 [1] Bioconduc~
## sparsevctrs 0.3.1 2025-03-17 [1] CRAN (R 4.6.0)
## spatial 7.3-18 2025-01-01 [2] CRAN (R 4.6.0)
## SpatialExperiment 1.17.0 2024-10-29 [1] Bioconduc~
## spatstat.data 3.1-6 2025-03-17 [1] CRAN (R 4.6.0)
## spatstat.explore 3.3-4 2025-01-08 [1] CRAN (R 4.6.0)
## spatstat.geom 3.3-6 2025-03-18 [1] CRAN (R 4.6.0)
## spatstat.random 3.3-2 2024-09-18 [1] CRAN (R 4.6.0)
## spatstat.sparse 3.1-0 2024-06-21 [1] CRAN (R 4.6.0)
## spatstat.univar 3.1-2 2025-03-05 [1] CRAN (R 4.6.0)
## spatstat.utils 3.1-3 2025-03-15 [1] CRAN (R 4.6.0)
## Spectra 1.17.9 2025-03-07 [1] Bioconduc~
## spelling 2.3.1 2024-10-04 [1] CRAN (R 4.6.0)
## splines 4.6.0 2025-03-15 [2] local
## splitstackshape 1.4.8 2019-04-21 [1] CRAN (R 4.6.0)
## SQUAREM 2021.1 2021-01-13 [1] CRAN (R 4.6.0)
## SRAdb 1.69.2 2024-12-10 [1] Bioconduc~
## stable 1.1.6 2022-03-02 [1] CRAN (R 4.6.0)
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##
## [1] /home/rsg/R/x86_64-pc-linux-gnu-library/4.6
## [2] /opt/R/R-devel/library
## * ββ Packages attached to the search path.
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## βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββEpigenomics Workshop
Welcome
Package: NGS-Physalia
Authors: Jacques Serizay [aut, cre]
Compiled: 2025-04-18
Package version: 0.99.0
R version: R Under development (unstable) (2025-03-14 r87973)
BioC version: 3.21
License: MIT + file LICENSE
This is the landing page for the βEpigenomics Data Analysisβ workshop, ed. 2025.
What
This course will introduce biologists and bioinformaticians to the field of regulatory epigenomics. We will cover a range of software and analysis workflows for processing and quantitative analysis of ChIP-seq, MNase and ATAC-seq data, RNA-seq, and Hi-C data. We will start by introducing general concepts about epigenomics. From there, we will then continue to describe the main analysis steps to go from raw sequencing data to processed and usable data. We will present classical analysis workflows, their output and the possible paths to investigate downstream of this. Towards the end of the workshop, we will focus on multi-omics data integration. Throughout the workshop, real-world datasets will be analysed using bash tools and R/Bioconductor packages.
Target audience
This course is primarily targeting researchers who are relatively new to the field of bioinformatics, with practical experience in the experimental side of epigenomics. Attendees should have a background in biology as well as be familiar with genomic data and common file formats from NGS sequencing experiments (fastq, BAM, BED).
Practical exercises will use command-line Linux and R code and will be presented as notebooks to ensure reproducible coding. Attendees are expected to know the basics of the R programming language and have prior expe- rience with the Unix command line.
Why
By the end of the course, participants will be able to:
- Understand the principles and experimental designs of key genomic assays.
- Perform preprocessing, alignment, and quality control for RNA-seq, ATAC-seq, ChIP-seq, and Hi-C data.
- Conduct downstream analyses such as differential expression, peak calling, motif analysis, and interaction visualization.
- Integrate multiple genomic data types to derive biological insights.
Instructors
Session info
Click to expand π