References
5.6 sessionInfo
sessionInfo()## R version 4.0.3 (2020-10-10)
## Platform: x86_64-conda-linux-gnu (64-bit)
## Running under: Scientific Linux 7.9 (Nitrogen)
##
## Matrix products: default
## BLAS/LAPACK: /home/ssg29/miniconda3/envs/bioc3.12/lib/libopenblasp-r0.3.12.so
##
## locale:
## [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
## [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] org.Hs.eg.db_3.12.0 TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0
## [3] GenomicFeatures_1.42.1 AnnotationDbi_1.52.0
## [5] ReactomePA_1.34.0 clusterProfiler_3.18.1
## [7] ChIPseeker_1.26.0 ggplot2_3.3.3
## [9] kableExtra_1.3.1 DiffBind_3.0.13
## [11] SummarizedExperiment_1.20.0 Biobase_2.50.0
## [13] MatrixGenerics_1.2.1 matrixStats_0.58.0
## [15] GenomicRanges_1.42.0 GenomeInfoDb_1.26.2
## [17] IRanges_2.24.1 S4Vectors_0.28.1
## [19] BiocGenerics_0.36.0 BiocParallel_1.24.1
## [21] yaml_2.2.1 nvimcom_0.9-106
## [23] data.table_1.13.6 colorout_1.2-2
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.1.0 htmlwidgets_1.5.3
## [3] RSQLite_2.2.3 grid_4.0.3
## [5] scatterpie_0.1.5 munsell_0.5.0
## [7] base64url_1.4 DT_0.17
## [9] systemPipeR_1.24.3 withr_2.4.1
## [11] colorspace_2.0-0 GOSemSim_2.16.1
## [13] Category_2.56.0 highr_0.8
## [15] knitr_1.31 rstudioapi_0.13
## [17] ggsignif_0.6.0 DOSE_3.16.0
## [19] labeling_0.4.2 bbmle_1.0.23.1
## [21] GenomeInfoDbData_1.2.4 mixsqp_0.3-43
## [23] hwriter_1.3.2 polyclip_1.10-0
## [25] bit64_4.0.5 farver_2.0.3
## [27] pheatmap_1.0.12 downloader_0.4
## [29] coda_0.19-4 batchtools_0.9.15
## [31] vctrs_0.3.6 generics_0.1.0
## [33] xfun_0.21 BiocFileCache_1.14.0
## [35] R6_2.5.0 apeglm_1.12.0
## [37] graphlayouts_0.7.1 invgamma_1.1
## [39] locfit_1.5-9.4 rsvg_2.1
## [41] bitops_1.0-6 cachem_1.0.4
## [43] fgsea_1.16.0 DelayedArray_0.16.1
## [45] assertthat_0.2.1 scales_1.1.1
## [47] ggraph_2.0.4 enrichplot_1.10.2
## [49] gtable_0.3.0 tidygraph_1.2.0
## [51] rlang_0.4.10 genefilter_1.72.1
## [53] splines_4.0.3 rtracklayer_1.50.0
## [55] brew_1.0-6 checkmate_2.0.0
## [57] BiocManager_1.30.10 reshape2_1.4.4
## [59] crosstalk_1.1.1 backports_1.2.1
## [61] qvalue_2.22.0 RBGL_1.66.0
## [63] tools_4.0.3 bookdown_0.21
## [65] ellipsis_0.3.1 gplots_3.1.1
## [67] RColorBrewer_1.1-2 Rcpp_1.0.6
## [69] plyr_1.8.6 progress_1.2.2
## [71] zlibbioc_1.36.0 purrr_0.3.4
## [73] RCurl_1.98-1.2 prettyunits_1.1.1
## [75] openssl_1.4.3 viridis_0.5.1
## [77] cowplot_1.1.1 ashr_2.2-47
## [79] ggrepel_0.9.1 magrittr_2.0.1
## [81] DO.db_2.9 reactome.db_1.74.0
## [83] truncnorm_1.0-8 mvtnorm_1.1-1
## [85] SQUAREM_2021.1 amap_0.8-18
## [87] hms_1.0.0 evaluate_0.14
## [89] xtable_1.8-4 XML_3.99-0.5
## [91] emdbook_1.3.12 jpeg_0.1-8.1
## [93] gridExtra_2.3 compiler_4.0.3
## [95] biomaRt_2.46.3 bdsmatrix_1.3-4
## [97] tibble_3.0.6 shadowtext_0.0.7
## [99] KernSmooth_2.23-18 V8_3.4.0
## [101] crayon_1.4.1 htmltools_0.5.1.1
## [103] GOstats_2.56.0 geneplotter_1.68.0
## [105] tidyr_1.1.2 DBI_1.1.1
## [107] tweenr_1.0.1 dbplyr_2.1.0
## [109] MASS_7.3-53.1 rappdirs_0.3.3
## [111] boot_1.3-27 ShortRead_1.48.0
## [113] Matrix_1.3-2 igraph_1.2.6
## [115] pkgconfig_2.0.3 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [117] rvcheck_0.1.8 GenomicAlignments_1.26.0
## [119] numDeriv_2016.8-1.1 xml2_1.3.2
## [121] annotate_1.68.0 webshot_0.5.2
## [123] XVector_0.30.0 AnnotationForge_1.32.0
## [125] rvest_0.3.6 stringr_1.4.0
## [127] VariantAnnotation_1.36.0 digest_0.6.27
## [129] graph_1.68.0 Biostrings_2.58.0
## [131] rmarkdown_2.6 fastmatch_1.1-0
## [133] edgeR_3.32.1 GSEABase_1.52.1
## [135] GreyListChIP_1.22.0 curl_4.3
## [137] graphite_1.36.0 Rsamtools_2.6.0
## [139] gtools_3.8.2 rjson_0.2.20
## [141] lifecycle_1.0.0 jsonlite_1.7.2
## [143] viridisLite_0.3.0 askpass_1.1
## [145] limma_3.46.0 BSgenome_1.58.0
## [147] pillar_1.4.7 lattice_0.20-41
## [149] plotrix_3.8-1 fastmap_1.1.0
## [151] httr_1.4.2 survival_3.2-7
## [153] GO.db_3.12.1 glue_1.4.2
## [155] png_0.1-7 bit_4.0.4
## [157] Rgraphviz_2.34.0 ggforce_0.3.2
## [159] stringi_1.5.3 blob_1.2.1
## [161] DESeq2_1.30.0 latticeExtra_0.6-29
## [163] caTools_1.18.1 memoise_2.0.0
## [165] DOT_0.1 dplyr_1.0.4
## [167] irlba_2.3.3