sessioninfo::session_info(
installed.packages()[,"Package"],
include_base = TRUE
)
## β Session info ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
## setting value
## version R Under development (unstable) (2026-04-12 r89873)
## os Ubuntu 24.04.4 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2026-04-16
## pandoc 3.9.0.2 @ /usr/bin/ (via rmarkdown)
## quarto 1.9.37 @ /usr/local/bin/quarto
##
## β Packages ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
## package * version date (UTC) lib source
## abind 1.4-8 2024-09-12 [1] CRAN (R 4.7.0)
## AnnotationDbi 1.73.1 2026-04-08 [1] Bioconduc~
## ape 5.8-1 2024-12-16 [1] CRAN (R 4.7.0)
## aplot 0.2.9 2025-09-12 [1] CRAN (R 4.7.0)
## askpass 1.2.1 2024-10-04 [1] CRAN (R 4.7.0)
## backports 1.5.1 2026-04-03 [1] CRAN (R 4.7.0)
## base * 4.7.0 2026-04-13 [2] local
## base64enc 0.1-6 2026-02-02 [1] CRAN (R 4.7.0)
## beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.7.0)
## BH 1.90.0-1 2025-12-14 [1] CRAN (R 4.7.0)
## Biobase 2.71.0 2025-10-30 [1] Bioconduc~
## BiocBook 1.9.0 2025-10-31 [1] Bioconduc~
## BiocFileCache 3.1.0 2025-10-30 [1] Bioconduc~
## BiocGenerics 0.57.0 2025-10-30 [1] Bioconduc~
## BiocIO 1.21.0 2025-10-30 [1] Bioconduc~
## biocmake 1.3.1 2025-11-23 [1] Bioconduc~
## BiocManager 1.30.27 2025-11-14 [1] CRAN (R 4.7.0)
## BiocParallel 1.45.0 2025-10-30 [1] Bioconduc~
## BiocStyle 2.39.0 2025-10-30 [1] Bioconduc~
## BiocVersion 3.23.1 2025-10-30 [1] Bioconductor 3.23 (R 4.7.0)
## Biostrings 2.79.5 2026-03-06 [1] Bioconduc~
## bit 4.6.0 2025-03-06 [1] CRAN (R 4.7.0)
## bit64 4.6.0-1 2025-01-16 [1] CRAN (R 4.7.0)
## bitops 1.0-9 2024-10-03 [1] CRAN (R 4.7.0)
## blob 1.3.0 2026-01-14 [1] CRAN (R 4.7.0)
## bookdown 0.46 2025-12-05 [1] CRAN (R 4.7.0)
## boot 1.3-32 2025-08-29 [2] CRAN (R 4.7.0)
## brew 1.0-10 2023-12-16 [1] CRAN (R 4.7.0)
## brio 1.1.5 2024-04-24 [1] CRAN (R 4.7.0)
## broom 1.0.12 2026-01-27 [1] CRAN (R 4.7.0)
## BSgenome 1.79.1 2025-11-04 [1] Bioconduc~
## BSgenome.Celegans.UCSC.ce11 1.4.2 2026-04-16 [1] Bioconductor
## bslib 0.10.0 2026-01-26 [1] CRAN (R 4.7.0)
## cachem 1.1.0 2024-05-16 [1] CRAN (R 4.7.0)
## Cairo 1.7-0 2025-10-29 [1] CRAN (R 4.7.0)
## callr 3.7.6 2024-03-25 [1] CRAN (R 4.7.0)
## caTools 1.18.3 2024-09-04 [1] CRAN (R 4.7.0)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.7.0)
## ChIPseeker 1.47.1 2025-11-04 [1] Bioconduc~
## cigarillo 1.1.0 2025-10-31 [1] Bioconduc~
## class 7.3-23 2025-01-01 [2] CRAN (R 4.7.0)
## cli 3.6.6 2026-04-09 [1] CRAN (R 4.7.0)
## clipr 0.8.0 2022-02-22 [1] CRAN (R 4.7.0)
## cluster 2.1.8.2 2026-02-05 [2] CRAN (R 4.7.0)
## CodeDepends 0.6.7 2026-03-03 [1] CRAN (R 4.7.0)
## codetools 0.2-20 2024-03-31 [2] CRAN (R 4.7.0)
## commonmark 2.0.0 2025-07-07 [1] CRAN (R 4.7.0)
## compiler 4.7.0 2026-04-13 [2] local
## conflicted 1.2.0 2023-02-01 [1] CRAN (R 4.7.0)
## cowplot 1.2.0 2025-07-07 [1] CRAN (R 4.7.0)
## cpp11 0.5.4 2026-04-04 [1] CRAN (R 4.7.0)
## crayon 1.5.3 2024-06-20 [1] CRAN (R 4.7.0)
## credentials 2.0.3 2025-09-12 [1] CRAN (R 4.7.0)
## crosstalk 1.2.2 2025-08-26 [1] CRAN (R 4.7.0)
## curl 7.0.0 2025-08-19 [1] CRAN (R 4.7.0)
## data.table 1.18.2.1 2026-01-27 [1] CRAN (R 4.7.0)
## datasets * 4.7.0 2026-04-13 [2] local
## DBI 1.3.0 2026-02-25 [1] CRAN (R 4.7.0)
## dbplyr 2.5.2 2026-02-13 [1] CRAN (R 4.7.0)
## DelayedArray 0.37.1 2026-03-31 [1] Bioconduc~
## deldir 2.0-4 2024-02-28 [1] CRAN (R 4.7.0)
## desc 1.4.3 2023-12-10 [1] CRAN (R 4.7.0)
## DESeq2 1.51.7 2026-03-13 [1] Bioconduc~
## devtools 2.5.0 2026-03-14 [1] CRAN (R 4.7.0)
## diffobj 0.3.6 2025-04-21 [1] CRAN (R 4.7.0)
## digest 0.6.39 2025-11-19 [1] CRAN (R 4.7.0)
## dir.expiry 1.19.0 2025-10-30 [1] Bioconduc~
## DirichletMultinomial 1.53.0 2025-10-31 [1] Bioconduc~
## docopt 0.7.2 2025-03-25 [1] CRAN (R 4.7.0)
## DOSE 4.5.1 2025-12-23 [1] Bioconduc~
## dotCall64 1.2 2024-10-04 [1] CRAN (R 4.7.0)
## downlit 0.4.5 2025-11-14 [1] CRAN (R 4.7.0)
## dplyr 1.2.1 2026-04-03 [1] CRAN (R 4.7.0)
## dqrng 0.4.1 2024-05-28 [1] CRAN (R 4.7.0)
## dtplyr 1.3.3 2026-02-11 [1] CRAN (R 4.7.0)
## ellipsis 0.3.3 2026-04-04 [1] CRAN (R 4.7.0)
## enrichit 0.1.4 2026-04-08 [1] CRAN (R 4.7.0)
## enrichplot 1.31.5 2026-04-01 [1] Bioconduc~
## evaluate 1.0.5 2025-08-27 [1] CRAN (R 4.7.0)
## fansi 1.0.7 2025-11-19 [1] CRAN (R 4.7.0)
## farver 2.1.2 2024-05-13 [1] CRAN (R 4.7.0)
## fastDummies 1.7.5 2025-01-20 [1] CRAN (R 4.7.0)
## fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.7.0)
## filelock 1.0.3 2023-12-11 [1] CRAN (R 4.7.0)
## fitdistrplus 1.2-6 2026-01-24 [1] CRAN (R 4.7.0)
## FNN 1.1.4.1 2024-09-22 [1] CRAN (R 4.7.0)
## fontawesome 0.5.3 2024-11-16 [1] CRAN (R 4.7.0)
## fontBitstreamVera 0.1.1 2017-02-01 [1] CRAN (R 4.7.0)
## fontLiberation 0.1.0 2016-10-15 [1] CRAN (R 4.7.0)
## fontquiver 0.2.1 2017-02-01 [1] CRAN (R 4.7.0)
## forcats 1.0.1 2025-09-25 [1] CRAN (R 4.7.0)
## foreign 0.8-91 2026-01-29 [2] CRAN (R 4.7.0)
## formatR 1.14 2023-01-17 [1] CRAN (R 4.7.0)
## fs 2.0.1 2026-03-24 [1] CRAN (R 4.7.0)
## futile.logger 1.4.9 2025-12-29 [1] CRAN (R 4.7.0)
## futile.options 1.0.1 2018-04-20 [1] CRAN (R 4.7.0)
## future 1.70.0 2026-03-14 [1] CRAN (R 4.7.0)
## future.apply 1.20.2 2026-02-20 [1] CRAN (R 4.7.0)
## gargle 1.6.1 2026-01-29 [1] CRAN (R 4.7.0)
## gdtools 0.5.0 2026-02-09 [1] CRAN (R 4.7.0)
## generics 0.1.4 2025-05-09 [1] CRAN (R 4.7.0)
## GenomeInfoDb 1.47.2 2025-12-04 [1] Bioconduc~
## GenomicAlignments 1.47.0 2025-10-31 [1] Bioconduc~
## GenomicFeatures 1.63.2 2026-04-06 [1] Bioconduc~
## GenomicRanges 1.63.2 2026-04-07 [1] Bioconduc~
## gert 2.3.1 2026-01-11 [1] CRAN (R 4.7.0)
## ggbeeswarm 0.7.3 2025-11-29 [1] CRAN (R 4.7.0)
## ggforce 0.5.0 2025-06-18 [1] CRAN (R 4.7.0)
## ggfun 0.2.0 2025-07-15 [1] CRAN (R 4.7.0)
## ggiraph 0.9.6 2026-02-21 [1] CRAN (R 4.7.0)
## ggnewscale 0.5.2 2025-06-20 [1] CRAN (R 4.7.0)
## ggplot2 4.0.2 2026-02-03 [1] CRAN (R 4.7.0)
## ggplotify 0.1.3 2025-09-20 [1] CRAN (R 4.7.0)
## ggrastr 1.0.2 2023-06-01 [1] CRAN (R 4.7.0)
## ggrepel 0.9.8 2026-03-17 [1] CRAN (R 4.7.0)
## ggridges 0.5.7 2025-08-27 [1] CRAN (R 4.7.0)
## ggtangle 0.1.1 2026-01-16 [1] CRAN (R 4.7.0)
## ggtree 4.1.2 2026-04-09 [1] Bioconduc~
## gh 1.5.0 2025-05-26 [1] CRAN (R 4.7.0)
## gitcreds 0.1.2 2022-09-08 [1] CRAN (R 4.7.0)
## globals 0.19.1 2026-03-13 [1] CRAN (R 4.7.0)
## glue 1.8.0 2024-09-30 [1] CRAN (R 4.7.0)
## GO.db 3.23.1 2026-04-16 [1] Bioconductor
## goftest 1.2-3 2021-10-07 [1] CRAN (R 4.7.0)
## googledrive 2.1.2 2025-09-10 [1] CRAN (R 4.7.0)
## googlesheets4 1.1.2 2025-09-03 [1] CRAN (R 4.7.0)
## GOSemSim 2.37.2 2026-01-15 [1] Bioconduc~
## gplots 3.3.0 2025-11-30 [1] CRAN (R 4.7.0)
## gprofiler2 0.2.4 2025-11-11 [1] CRAN (R 4.7.0)
## graph 1.89.1 2025-12-02 [1] Bioconduc~
## graphics * 4.7.0 2026-04-13 [2] local
## grDevices * 4.7.0 2026-04-13 [2] local
## grid 4.7.0 2026-04-13 [2] local
## gridExtra 2.3 2017-09-09 [1] CRAN (R 4.7.0)
## gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.7.0)
## gtable 0.3.6 2024-10-25 [1] CRAN (R 4.7.0)
## gtools 3.9.5 2023-11-20 [1] CRAN (R 4.7.0)
## haven 2.5.5 2025-05-30 [1] CRAN (R 4.7.0)
## here 1.0.2 2025-09-15 [1] CRAN (R 4.7.0)
## HiCExperiment 1.11.0 2025-10-31 [1] Bioconduc~
## HiContacts 1.13.0 2025-10-31 [1] Bioconduc~
## highr 0.12 2026-03-06 [1] CRAN (R 4.7.0)
## hms 1.1.4 2025-10-17 [1] CRAN (R 4.7.0)
## htmltools 0.5.9 2025-12-04 [1] CRAN (R 4.7.0)
## htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.7.0)
## httpuv 1.6.17 2026-03-18 [1] CRAN (R 4.7.0)
## httr 1.4.8 2026-02-13 [1] CRAN (R 4.7.0)
## httr2 1.2.2 2025-12-08 [1] CRAN (R 4.7.0)
## ica 1.0-3 2022-07-08 [1] CRAN (R 4.7.0)
## ids 1.0.1 2017-05-31 [1] CRAN (R 4.7.0)
## igraph 2.2.3 2026-04-07 [1] CRAN (R 4.7.0)
## ini 0.3.1 2018-05-20 [1] CRAN (R 4.7.0)
## InteractionSet 1.39.0 2025-10-31 [1] Bioconduc~
## IRanges 2.45.0 2025-10-31 [1] Bioconduc~
## irlba 2.3.7 2026-01-30 [1] CRAN (R 4.7.0)
## isoband 0.3.0 2025-12-07 [1] CRAN (R 4.7.0)
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.7.0)
## jsonlite 2.0.0 2025-03-27 [1] CRAN (R 4.7.0)
## KEGGREST 1.51.1 2025-11-17 [1] Bioconduc~
## KernSmooth 2.23-26 2025-01-01 [2] CRAN (R 4.7.0)
## knitr 1.51 2025-12-20 [1] CRAN (R 4.7.0)
## labeling 0.4.3 2023-08-29 [1] CRAN (R 4.7.0)
## lambda.r 1.2.4 2019-09-18 [1] CRAN (R 4.7.0)
## later 1.4.8 2026-03-05 [1] CRAN (R 4.7.0)
## lattice 0.22-9 2026-02-09 [2] CRAN (R 4.7.0)
## lazyeval 0.2.3 2026-04-04 [1] CRAN (R 4.7.0)
## lifecycle 1.0.5 2026-01-08 [1] CRAN (R 4.7.0)
## listenv 0.10.1 2026-03-10 [1] CRAN (R 4.7.0)
## littler 0.3.23 2026-04-12 [1] CRAN (R 4.7.0)
## lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.7.0)
## locfit 1.5-9.12 2025-03-05 [1] CRAN (R 4.7.0)
## lubridate 1.9.5 2026-02-04 [1] CRAN (R 4.7.0)
## magick 2.9.1 2026-02-28 [1] CRAN (R 4.7.0)
## magrittr 2.0.5 2026-04-04 [1] CRAN (R 4.7.0)
## MASS 7.3-65 2025-02-28 [2] CRAN (R 4.7.0)
## Matrix 1.7-5 2026-03-21 [2] CRAN (R 4.7.0)
## MatrixGenerics 1.23.0 2025-10-30 [1] Bioconduc~
## matrixStats 1.5.0 2025-01-07 [1] CRAN (R 4.7.0)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.7.0)
## methods * 4.7.0 2026-04-13 [2] local
## mgcv 1.9-4 2025-11-07 [2] CRAN (R 4.7.0)
## mime 0.13 2025-03-17 [1] CRAN (R 4.7.0)
## miniUI 0.1.2 2025-04-17 [1] CRAN (R 4.7.0)
## modelr 0.1.11 2023-03-22 [1] CRAN (R 4.7.0)
## motifmatchr 1.33.0 2025-11-04 [1] Bioconduc~
## NGSPhysalia 0.99.0 2026-04-16 [1] local
## nlme 3.1-169 2026-03-27 [2] CRAN (R 4.7.0)
## nnet 7.3-20 2025-01-01 [2] CRAN (R 4.7.0)
## openssl 2.3.5 2026-02-26 [1] CRAN (R 4.7.0)
## otel 0.2.0 2025-08-29 [1] CRAN (R 4.7.0)
## pak 0.9.3-1 2026-04-09 [1] CRAN (R 4.7.0)
## parallel 4.7.0 2026-04-13 [2] local
## parallelly 1.46.1 2026-01-08 [1] CRAN (R 4.7.0)
## patchwork 1.3.2 2025-08-25 [1] CRAN (R 4.7.0)
## pbapply 1.7-4 2025-07-20 [1] CRAN (R 4.7.0)
## pillar 1.11.1 2025-09-17 [1] CRAN (R 4.7.0)
## pkgbuild 1.4.8 2025-05-26 [1] CRAN (R 4.7.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.7.0)
## pkgdown 2.2.0 2025-11-06 [1] CRAN (R 4.7.0)
## pkgload 1.5.1 2026-04-01 [1] CRAN (R 4.7.0)
## plotly 4.12.0 2026-01-24 [1] CRAN (R 4.7.0)
## plotrix 3.8-14 2026-02-13 [1] CRAN (R 4.7.0)
## plyinteractions 1.9.2 2026-01-11 [1] Bioconduc~
## plyr 1.8.9 2023-10-02 [1] CRAN (R 4.7.0)
## plyranges 1.31.7 2026-04-02 [1] Bioconduc~
## plyxp 1.5.0 2025-10-31 [1] Bioconduc~
## png 0.1-9 2026-03-15 [1] CRAN (R 4.7.0)
## polyclip 1.10-7 2024-07-23 [1] CRAN (R 4.7.0)
## praise 1.0.0 2015-08-11 [1] CRAN (R 4.7.0)
## preprocessCore 1.73.0 2025-10-30 [1] Bioconductor 3.23 (R 4.7.0)
## prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.7.0)
## processx 3.8.7 2026-04-01 [1] CRAN (R 4.7.0)
## profvis 0.4.0 2024-09-20 [1] CRAN (R 4.7.0)
## progress 1.2.3 2023-12-06 [1] CRAN (R 4.7.0)
## progressr 0.19.0 2026-03-31 [1] CRAN (R 4.7.0)
## promises 1.5.0 2025-11-01 [1] CRAN (R 4.7.0)
## ps 1.9.2 2026-03-31 [1] CRAN (R 4.7.0)
## purrr 1.2.2 2026-04-10 [1] CRAN (R 4.7.0)
## pwalign 1.7.0 2025-10-31 [1] Bioconduc~
## quarto 1.5.1 2025-09-04 [1] CRAN (R 4.7.0)
## R6 2.6.1 2025-02-15 [1] CRAN (R 4.7.0)
## ragg 1.5.2 2026-03-23 [1] CRAN (R 4.7.0)
## RANN 2.6.2 2024-08-25 [1] CRAN (R 4.7.0)
## rappdirs 0.3.4 2026-01-17 [1] CRAN (R 4.7.0)
## rcmdcheck 1.4.0 2021-09-27 [1] CRAN (R 4.7.0)
## RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.7.0)
## Rcpp 1.1.1 2026-01-10 [1] CRAN (R 4.7.0)
## RcppAnnoy 0.0.23 2026-01-12 [1] CRAN (R 4.7.0)
## RcppArmadillo 15.2.4-1 2026-03-17 [1] CRAN (R 4.7.0)
## RcppEigen 0.3.4.0.2 2024-08-24 [1] CRAN (R 4.7.0)
## RcppHNSW 0.6.0 2024-02-04 [1] CRAN (R 4.7.0)
## RcppProgress 0.4.2 2020-02-06 [1] CRAN (R 4.7.0)
## RcppThread 2.3.0 2026-01-16 [1] CRAN (R 4.7.0)
## RcppTOML 0.2.3 2025-03-08 [1] CRAN (R 4.7.0)
## RCurl 1.98-1.18 2026-03-21 [1] CRAN (R 4.7.0)
## readr 2.2.0 2026-02-19 [1] CRAN (R 4.7.0)
## readxl 1.4.5 2025-03-07 [1] CRAN (R 4.7.0)
## rebook 1.21.0 2025-11-02 [1] Bioconduc~
## rematch 2.0.0 2023-08-30 [1] CRAN (R 4.7.0)
## rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.7.0)
## renv 1.2.2 2026-04-16 [1] CRAN (R 4.7.0)
## reprex 2.1.1 2024-07-06 [1] CRAN (R 4.7.0)
## reshape2 1.4.5 2025-11-12 [1] CRAN (R 4.7.0)
## restfulr 0.0.16 2025-06-27 [1] CRAN (R 4.7.0)
## reticulate 1.46.0 2026-04-09 [1] CRAN (R 4.7.0)
## rhdf5 2.55.16 2026-03-12 [1] Bioconduc~
## rhdf5filters 1.23.3 2025-12-07 [1] Bioconduc~
## Rhdf5lib 1.33.6 2026-03-16 [1] Bioconduc~
## Rhtslib 3.7.0 2025-10-30 [1] Bioconduc~
## rjson 0.2.23 2024-09-16 [1] CRAN (R 4.7.0)
## rlang 1.2.0 2026-04-06 [1] CRAN (R 4.7.0)
## rmarkdown 2.31 2026-03-26 [1] CRAN (R 4.7.0)
## ROCR 1.0-12 2026-01-23 [1] CRAN (R 4.7.0)
## roxygen2 7.3.3 2025-09-03 [1] CRAN (R 4.7.0)
## rpart 4.1.27 2026-03-27 [2] CRAN (R 4.7.0)
## rprojroot 2.1.1 2025-08-26 [1] CRAN (R 4.7.0)
## Rsamtools 2.27.2 2026-04-09 [1] Bioconduc~
## RSpectra 0.16-2 2024-07-18 [1] CRAN (R 4.7.0)
## RSQLite 2.4.6 2026-02-06 [1] CRAN (R 4.7.0)
## rstudioapi 0.18.0 2026-01-16 [1] CRAN (R 4.7.0)
## rtracklayer 1.71.3 2025-12-14 [1] Bioconduc~
## Rtsne 0.17 2023-12-07 [1] CRAN (R 4.7.0)
## rversions 3.0.0 2025-10-09 [1] CRAN (R 4.7.0)
## rvest 1.0.5 2025-08-29 [1] CRAN (R 4.7.0)
## S4Arrays 1.11.1 2025-11-25 [1] Bioconduc~
## S4Vectors 0.49.1-1 2026-04-05 [1] Bioconduc~
## S7 0.2.1-1 2025-11-14 [1] CRAN (R 4.7.0)
## sass 0.4.10 2025-04-11 [1] CRAN (R 4.7.0)
## scales 1.4.0 2025-04-24 [1] CRAN (R 4.7.0)
## scattermore 1.2 2023-06-12 [1] CRAN (R 4.7.0)
## scatterpie 0.2.6 2025-09-12 [1] CRAN (R 4.7.0)
## sctransform 0.4.3 2026-01-10 [1] CRAN (R 4.7.0)
## selectr 0.5-1 2025-12-17 [1] CRAN (R 4.7.0)
## Seqinfo 1.1.0 2025-10-31 [1] Bioconduc~
## seqLogo 1.77.0 2025-10-30 [1] Bioconduc~
## sessioninfo 1.2.3 2025-02-05 [1] CRAN (R 4.7.0)
## Seurat 5.4.0 2025-12-14 [1] CRAN (R 4.7.0)
## SeuratObject 5.4.0 2026-04-11 [1] CRAN (R 4.7.0)
## shiny 1.13.0 2026-02-20 [1] CRAN (R 4.7.0)
## SingleCellExperiment 1.33.2 2026-03-24 [1] Bioconduc~
## sitmo 2.0.2 2021-10-13 [1] CRAN (R 4.7.0)
## snow 0.4-4 2021-10-27 [1] CRAN (R 4.7.0)
## sourcetools 0.1.7-2 2026-03-28 [1] CRAN (R 4.7.0)
## sp 2.2-1 2026-02-13 [1] CRAN (R 4.7.0)
## spam 2.11-3 2026-01-08 [1] CRAN (R 4.7.0)
## SparseArray 1.11.13 2026-04-01 [1] Bioconduc~
## spatial 7.3-18 2025-01-01 [2] CRAN (R 4.7.0)
## SpatialExperiment 1.21.0 2025-11-03 [1] Bioconduc~
## spatstat.data 3.1-9 2025-10-18 [1] CRAN (R 4.7.0)
## spatstat.explore 3.8-0 2026-03-22 [1] CRAN (R 4.7.0)
## spatstat.geom 3.7-3 2026-03-23 [1] CRAN (R 4.7.0)
## spatstat.random 3.4-5 2026-03-22 [1] CRAN (R 4.7.0)
## spatstat.sparse 3.1-0 2024-06-21 [1] CRAN (R 4.7.0)
## spatstat.univar 3.1-7 2026-03-18 [1] CRAN (R 4.7.0)
## spatstat.utils 3.2-2 2026-03-10 [1] CRAN (R 4.7.0)
## splines 4.7.0 2026-04-13 [2] local
## stats * 4.7.0 2026-04-13 [2] local
## stats4 4.7.0 2026-04-13 [2] local
## strawr 0.0.92 2024-07-16 [1] CRAN (R 4.7.0)
## stringi 1.8.7 2025-03-27 [1] CRAN (R 4.7.0)
## stringr 1.6.0 2025-11-04 [1] CRAN (R 4.7.0)
## SummarizedExperiment 1.41.1 2026-02-06 [1] Bioconduc~
## survival 3.8-6 2026-01-16 [2] CRAN (R 4.7.0)
## sys 3.4.3 2024-10-04 [1] CRAN (R 4.7.0)
## systemfonts 1.3.2 2026-03-05 [1] CRAN (R 4.7.0)
## tcltk 4.7.0 2026-04-13 [2] local
## tensor 1.5.1 2025-06-17 [1] CRAN (R 4.7.0)
## testthat 3.3.2 2026-01-11 [1] CRAN (R 4.7.0)
## textshaping 1.0.5 2026-03-06 [1] CRAN (R 4.7.0)
## TFBSTools 1.49.0 2025-11-04 [1] Bioconduc~
## TFMPvalue 1.0.0 2026-01-19 [1] CRAN (R 4.7.0)
## tibble 3.3.1 2026-01-11 [1] CRAN (R 4.7.0)
## tidyCoverage 1.7.1 2026-01-07 [1] Bioconduc~
## tidydr 0.0.6 2025-07-25 [1] CRAN (R 4.7.0)
## tidygate 1.0.19 2025-12-10 [1] CRAN (R 4.7.0)
## tidyomics 1.7.0 2025-11-04 [1] Bioconduc~
## tidyr 1.3.2 2025-12-19 [1] CRAN (R 4.7.0)
## tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.7.0)
## tidyseurat 0.8.10 2026-02-26 [1] CRAN (R 4.7.0)
## tidySingleCellExperiment 1.21.0 2025-11-03 [1] Bioconduc~
## tidySpatialExperiment 1.7.2 2025-12-01 [1] Bioconduc~
## tidySummarizedExperiment 1.21.0 2025-10-31 [1] Bioconduc~
## tidytree 0.4.7 2026-01-08 [1] CRAN (R 4.7.0)
## tidyverse 2.0.0 2023-02-22 [1] CRAN (R 4.7.0)
## timechange 0.4.0 2026-01-29 [1] CRAN (R 4.7.0)
## tinytex 0.59 2026-03-28 [1] CRAN (R 4.7.0)
## tools 4.7.0 2026-04-13 [2] local
## treeio 1.35.0 2025-10-30 [1] Bioconduc~
## ttservice 0.5.3 2025-07-10 [1] CRAN (R 4.7.0)
## tweenr 2.0.3 2024-02-26 [1] CRAN (R 4.7.0)
## TxDb.Celegans.UCSC.ce11.ensGene 3.15.0 2026-04-16 [1] Bioconductor
## TxDb.Hsapiens.UCSC.hg19.knownGene 3.22.1 2026-04-16 [1] Bioconductor
## tzdb 0.5.0 2025-03-15 [1] CRAN (R 4.7.0)
## UCSC.utils 1.7.1 2025-12-09 [1] Bioconduc~
## universalmotif 1.29.2 2026-04-10 [1] Bioconduc~
## urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.7.0)
## usethis 3.2.1 2025-09-06 [1] CRAN (R 4.7.0)
## utf8 1.2.6 2025-06-08 [1] CRAN (R 4.7.0)
## utils * 4.7.0 2026-04-13 [2] local
## uuid 1.2-2 2026-01-23 [1] CRAN (R 4.7.0)
## uwot 0.2.4 2025-11-10 [1] CRAN (R 4.7.0)
## vctrs 0.7.3 2026-04-11 [1] CRAN (R 4.7.0)
## vipor 0.4.7 2023-12-18 [1] CRAN (R 4.7.0)
## viridis 0.6.5 2024-01-29 [1] CRAN (R 4.7.0)
## viridisLite 0.4.3 2026-02-04 [1] CRAN (R 4.7.0)
## vroom 1.7.1 2026-03-31 [1] CRAN (R 4.7.0)
## waldo 0.6.2 2025-07-11 [1] CRAN (R 4.7.0)
## whisker 0.4.1 2022-12-05 [1] CRAN (R 4.7.0)
## withr 3.0.2 2024-10-28 [1] CRAN (R 4.7.0)
## xfun 0.57 2026-03-20 [1] CRAN (R 4.7.0)
## XML 3.99-0.23 2026-03-20 [1] CRAN (R 4.7.0)
## xml2 1.5.2 2026-01-17 [1] CRAN (R 4.7.0)
## xopen 1.0.1 2024-04-25 [1] CRAN (R 4.7.0)
## xtable 1.8-8 2026-02-22 [1] CRAN (R 4.7.0)
## XVector 0.51.0 2025-10-31 [1] Bioconduc~
## yaml 2.3.12 2025-12-10 [1] CRAN (R 4.7.0)
## yulab.utils 0.2.4 2026-02-02 [1] CRAN (R 4.7.0)
## zip 2.3.3 2025-05-13 [1] CRAN (R 4.7.0)
## zoo 1.8-15 2025-12-15 [1] CRAN (R 4.7.0)
##
## [1] /usr/local/lib/R/site-library
## [2] /usr/local/lib/R/library
## * ββ Packages attached to the search path.
##
## β Python configuration ββββββββββββββββββββββββββββββββββββββββββββββββββββ
## Python is not available
##
## βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββEpigenomics Workshop
Welcome
Package: NGSPhysalia
Authors: Jacques Serizay [aut, cre]
Compiled: 2026-04-16
Package version: 0.99.0
R version: R Under development (unstable) (2026-04-12 r89873)
BioC version: 3.23
License: MIT + file LICENSE
This is the landing page for the βEpigenomics Data Analysisβ workshop, ed. 2026.
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
NoteClick to expand π