sessionInfo()
#> R version 4.4.1 (2024-06-14)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Sonoma 14.5
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> time zone: UTC
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] BIUMmisc_0.2.0
#>
#> loaded via a namespace (and not attached):
#> [1] splines_4.4.1 later_1.3.2
#> [3] BiocIO_1.15.0 filelock_1.0.3
#> [5] bitops_1.0-7 ggplotify_0.1.2
#> [7] BiasedUrn_2.0.12 tibble_3.2.1
#> [9] polyclip_1.10-6 graph_1.83.0
#> [11] XML_3.99-0.17 httr2_1.0.1
#> [13] lifecycle_1.0.4 topGO_2.57.0
#> [15] doParallel_1.0.17 lattice_0.22-6
#> [17] MASS_7.3-61 mosdef_1.1.0
#> [19] dendextend_1.17.1 magrittr_2.0.3
#> [21] plotly_4.10.4 sass_0.4.9
#> [23] rmarkdown_2.27 jquerylib_0.1.4
#> [25] yaml_2.3.9 httpuv_1.6.15
#> [27] sessioninfo_1.2.2 cowplot_1.1.3
#> [29] DBI_1.2.3 RColorBrewer_1.1-3
#> [31] abind_1.4-5 zlibbioc_1.51.1
#> [33] expm_0.999-9 GenomicRanges_1.57.1
#> [35] purrr_1.0.2 RCurl_1.98-1.14
#> [37] ggraph_2.2.1 BiocGenerics_0.51.0
#> [39] yulab.utils_0.1.4 rappdirs_0.3.3
#> [41] tweenr_2.0.3 circlize_0.4.16
#> [43] GenomeInfoDbData_1.2.12 IRanges_2.39.1
#> [45] S4Vectors_0.43.1 enrichplot_1.25.0
#> [47] ggrepel_0.9.5 tidytree_0.4.6
#> [49] pkgdown_2.1.0.9000 codetools_0.2-20
#> [51] DelayedArray_0.31.6 xml2_1.3.6
#> [53] DOSE_3.31.2 DT_0.33
#> [55] bs4Dash_2.3.3 ggforce_0.4.2
#> [57] tidyselect_1.2.1 shape_1.4.6.1
#> [59] aplot_0.2.3 UCSC.utils_1.1.0
#> [61] farver_2.1.2 goseq_1.57.2
#> [63] viridis_0.6.5 ComplexUpset_1.3.3
#> [65] GeneTonic_2.9.0 shinyWidgets_0.8.6
#> [67] BiocFileCache_2.13.0 matrixStats_1.3.0
#> [69] stats4_4.4.1 dynamicTreeCut_1.63-1
#> [71] GenomicAlignments_1.41.0 jsonlite_1.8.8
#> [73] GetoptLong_1.0.5 tidygraph_1.3.1
#> [75] ggridges_0.5.6 iterators_1.0.14
#> [77] systemfonts_1.1.0 foreach_1.5.2
#> [79] progress_1.2.3 tools_4.4.1
#> [81] treeio_1.29.0 ragg_1.3.2
#> [83] Rcpp_1.0.12 glue_1.7.0
#> [85] gridExtra_2.3 SparseArray_1.5.17
#> [87] mgcv_1.9-1 geneLenDataBase_1.41.2
#> [89] xfun_0.45 DESeq2_1.45.0
#> [91] qvalue_2.37.0 MatrixGenerics_1.17.0
#> [93] GenomeInfoDb_1.41.1 dplyr_1.1.4
#> [95] withr_3.0.0 fastmap_1.2.0
#> [97] fansi_1.0.6 SparseM_1.84
#> [99] digest_0.6.36 R6_2.5.1
#> [101] mime_0.12 gridGraphics_0.5-1
#> [103] textshaping_0.4.0 colorspace_2.1-0
#> [105] GO.db_3.19.1 biomaRt_2.61.2
#> [107] RSQLite_2.3.7 utf8_1.2.4
#> [109] tidyr_1.3.1 generics_0.1.3
#> [111] data.table_1.15.4 rtracklayer_1.65.0
#> [113] prettyunits_1.2.0 graphlayouts_1.1.1
#> [115] httr_1.4.7 htmlwidgets_1.6.4
#> [117] S4Arrays_1.5.3 scatterpie_0.2.3
#> [119] pkgconfig_2.0.3 gtable_0.3.5
#> [121] blob_1.2.4 ComplexHeatmap_2.21.0
#> [123] XVector_0.45.0 clusterProfiler_4.13.0
#> [125] shadowtext_0.1.3 htmltools_0.5.8.1
#> [127] fgsea_1.31.0 rintrojs_0.3.4
#> [129] clue_0.3-65 scales_1.3.0
#> [131] Biobase_2.65.0 png_0.1-8
#> [133] ggfun_0.1.5 rstudioapi_0.16.0
#> [135] knitr_1.48 reshape2_1.4.4
#> [137] rjson_0.2.21 curl_5.2.1
#> [139] visNetwork_2.1.2 nlme_3.1-165
#> [141] shinyAce_0.4.2 cachem_1.1.0
#> [143] GlobalOptions_0.1.2 stringr_1.5.1
#> [145] backbone_2.1.4 parallel_4.4.1
#> [147] miniUI_0.1.1.1 HDO.db_0.99.1
#> [149] shinycssloaders_1.0.0 AnnotationDbi_1.67.0
#> [151] restfulr_0.0.15 desc_1.4.3
#> [153] pillar_1.9.0 grid_4.4.1
#> [155] vctrs_0.6.5 promises_1.3.0
#> [157] tippy_0.1.0 dbplyr_2.5.0
#> [159] xtable_1.8-4 cluster_2.1.6
#> [161] evaluate_0.24.0 GenomicFeatures_1.57.0
#> [163] Rsamtools_2.21.0 cli_3.6.3
#> [165] locfit_1.5-9.10 compiler_4.4.1
#> [167] rlang_1.1.4 crayon_1.5.3
#> [169] plyr_1.8.9 fs_1.6.4
#> [171] stringi_1.8.4 viridisLite_0.4.2
#> [173] BiocParallel_1.39.0 txdbmaker_1.1.1
#> [175] munsell_0.5.1 Biostrings_2.73.1
#> [177] lazyeval_0.2.2 colourpicker_1.3.0
#> [179] GOSemSim_2.31.0 Matrix_1.7-0
#> [181] hms_1.1.3 patchwork_1.2.0
#> [183] bit64_4.0.5 ggplot2_3.5.1
#> [185] KEGGREST_1.45.1 shiny_1.8.1.1
#> [187] SummarizedExperiment_1.35.1 igraph_2.0.3
#> [189] memoise_2.0.1 bslib_0.7.0
#> [191] ggtree_3.13.0 fastmatch_1.1-4
#> [193] bit_4.0.5 gson_0.1.0
#> [195] ape_5.8
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.1 (2024-06-14)
#> os macOS Sonoma 14.5
#> system aarch64, darwin20
#> ui X11
#> language en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz UTC
#> date 2024-07-10
#> pandoc 3.1.11 @ /usr/local/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> abind 1.4-5 2016-07-21 [1] CRAN (R 4.4.0)
#> AnnotationDbi 1.67.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> ape 5.8 2024-04-11 [1] CRAN (R 4.4.0)
#> aplot 0.2.3 2024-06-17 [1] CRAN (R 4.4.0)
#> backbone 2.1.4 2024-05-09 [1] CRAN (R 4.4.0)
#> BiasedUrn 2.0.12 2024-06-16 [1] CRAN (R 4.4.0)
#> Biobase 2.65.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> BiocFileCache 2.13.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> BiocGenerics 0.51.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> BiocIO 1.15.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> BiocParallel 1.39.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> biomaRt 2.61.2 2024-06-24 [1] Bioconductor 3.20 (R 4.4.1)
#> Biostrings 2.73.1 2024-06-02 [1] Bioconductor 3.20 (R 4.4.0)
#> bit 4.0.5 2022-11-15 [1] CRAN (R 4.4.0)
#> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.4.0)
#> bitops 1.0-7 2021-04-24 [1] CRAN (R 4.4.0)
#> BIUMmisc * 0.2.0 2024-07-10 [1] local
#> blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.0)
#> bs4Dash 2.3.3 2024-01-23 [1] CRAN (R 4.4.0)
#> bslib 0.7.0 2024-03-29 [1] CRAN (R 4.4.0)
#> cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0)
#> circlize 0.4.16 2024-02-20 [1] CRAN (R 4.4.0)
#> cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.0)
#> clue 0.3-65 2023-09-23 [1] CRAN (R 4.4.0)
#> cluster 2.1.6 2023-12-01 [2] CRAN (R 4.4.1)
#> clusterProfiler 4.13.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> codetools 0.2-20 2024-03-31 [2] CRAN (R 4.4.1)
#> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.4.0)
#> colourpicker 1.3.0 2023-08-21 [1] CRAN (R 4.4.0)
#> ComplexHeatmap 2.21.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> ComplexUpset 1.3.3 2021-12-11 [1] CRAN (R 4.4.0)
#> cowplot 1.1.3 2024-01-22 [1] CRAN (R 4.4.0)
#> crayon 1.5.3 2024-06-20 [1] CRAN (R 4.4.0)
#> curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.0)
#> data.table 1.15.4 2024-03-30 [1] CRAN (R 4.4.0)
#> DBI 1.2.3 2024-06-02 [1] CRAN (R 4.4.0)
#> dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.4.0)
#> DelayedArray 0.31.6 2024-07-05 [1] Bioconductor 3.20 (R 4.4.1)
#> dendextend 1.17.1 2023-03-25 [1] CRAN (R 4.4.0)
#> desc 1.4.3 2023-12-10 [1] CRAN (R 4.4.0)
#> DESeq2 1.45.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> digest 0.6.36 2024-06-23 [1] CRAN (R 4.4.0)
#> doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.4.0)
#> DOSE 3.31.2 2024-06-14 [1] Bioconductor 3.20 (R 4.4.1)
#> dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.4.0)
#> DT 0.33 2024-04-04 [1] CRAN (R 4.4.0)
#> dynamicTreeCut 1.63-1 2016-03-11 [1] CRAN (R 4.4.0)
#> enrichplot 1.25.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> evaluate 0.24.0 2024-06-10 [1] CRAN (R 4.4.0)
#> expm 0.999-9 2024-01-11 [1] CRAN (R 4.4.0)
#> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0)
#> farver 2.1.2 2024-05-13 [1] CRAN (R 4.4.0)
#> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
#> fastmatch 1.1-4 2023-08-18 [1] CRAN (R 4.4.0)
#> fgsea 1.31.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> filelock 1.0.3 2023-12-11 [1] CRAN (R 4.4.0)
#> foreach 1.5.2 2022-02-02 [1] CRAN (R 4.4.0)
#> fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0)
#> geneLenDataBase 1.41.2 2024-06-13 [1] Bioconductor 3.20 (R 4.4.1)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0)
#> GeneTonic 2.9.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> GenomeInfoDb 1.41.1 2024-06-12 [1] Bioconductor 3.20 (R 4.4.1)
#> GenomeInfoDbData 1.2.12 2024-07-10 [1] Bioconductor
#> GenomicAlignments 1.41.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> GenomicFeatures 1.57.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> GenomicRanges 1.57.1 2024-06-12 [1] Bioconductor 3.20 (R 4.4.1)
#> GetoptLong 1.0.5 2020-12-15 [1] CRAN (R 4.4.0)
#> ggforce 0.4.2 2024-02-19 [1] CRAN (R 4.4.0)
#> ggfun 0.1.5 2024-05-28 [1] CRAN (R 4.4.0)
#> ggplot2 3.5.1 2024-04-23 [1] CRAN (R 4.4.0)
#> ggplotify 0.1.2 2023-08-09 [1] CRAN (R 4.4.0)
#> ggraph 2.2.1 2024-03-07 [1] CRAN (R 4.4.0)
#> ggrepel 0.9.5 2024-01-10 [1] CRAN (R 4.4.0)
#> ggridges 0.5.6 2024-01-23 [1] CRAN (R 4.4.0)
#> ggtree 3.13.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.4.0)
#> glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0)
#> GO.db 3.19.1 2024-07-10 [1] Bioconductor
#> GOSemSim 2.31.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> goseq 1.57.2 2024-06-12 [1] Bioconductor 3.20 (R 4.4.1)
#> graph 1.83.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> graphlayouts 1.1.1 2024-03-09 [1] CRAN (R 4.4.0)
#> gridExtra 2.3 2017-09-09 [1] CRAN (R 4.4.0)
#> gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.4.0)
#> gson 0.1.0 2023-03-07 [1] CRAN (R 4.4.0)
#> gtable 0.3.5 2024-04-22 [1] CRAN (R 4.4.0)
#> HDO.db 0.99.1 2024-07-10 [1] Bioconductor
#> hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
#> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#> htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0)
#> httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0)
#> httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0)
#> httr2 1.0.1 2024-04-01 [1] CRAN (R 4.4.0)
#> igraph 2.0.3 2024-03-13 [1] CRAN (R 4.4.0)
#> IRanges 2.39.1 2024-07-03 [1] Bioconductor 3.20 (R 4.4.1)
#> iterators 1.0.14 2022-02-05 [1] CRAN (R 4.4.0)
#> jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.4.0)
#> jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.4.0)
#> KEGGREST 1.45.1 2024-06-18 [1] Bioconductor 3.20 (R 4.4.1)
#> knitr 1.48 2024-07-07 [1] CRAN (R 4.4.0)
#> later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0)
#> lattice 0.22-6 2024-03-20 [2] CRAN (R 4.4.1)
#> lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.4.0)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
#> locfit 1.5-9.10 2024-06-24 [1] CRAN (R 4.4.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
#> MASS 7.3-61 2024-06-13 [1] CRAN (R 4.4.0)
#> Matrix 1.7-0 2024-04-26 [2] CRAN (R 4.4.1)
#> MatrixGenerics 1.17.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> matrixStats 1.3.0 2024-04-11 [1] CRAN (R 4.4.0)
#> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0)
#> mgcv 1.9-1 2023-12-21 [2] CRAN (R 4.4.1)
#> mime 0.12 2021-09-28 [1] CRAN (R 4.4.0)
#> miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0)
#> mosdef 1.1.0 2024-06-05 [1] Bioconductor 3.20 (R 4.4.0)
#> munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.0)
#> nlme 3.1-165 2024-06-06 [1] CRAN (R 4.4.0)
#> patchwork 1.2.0 2024-01-08 [1] CRAN (R 4.4.0)
#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
#> pkgdown 2.1.0.9000 2024-07-10 [1] Github (r-lib/pkgdown@f20a649)
#> plotly 4.10.4 2024-01-13 [1] CRAN (R 4.4.0)
#> plyr 1.8.9 2023-10-02 [1] CRAN (R 4.4.0)
#> png 0.1-8 2022-11-29 [1] CRAN (R 4.4.0)
#> polyclip 1.10-6 2023-09-27 [1] CRAN (R 4.4.0)
#> prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.4.0)
#> progress 1.2.3 2023-12-06 [1] CRAN (R 4.4.0)
#> promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0)
#> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0)
#> qvalue 2.37.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0)
#> ragg 1.3.2 2024-05-15 [1] CRAN (R 4.4.0)
#> rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.4.0)
#> RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.4.0)
#> Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.0)
#> RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.4.0)
#> reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.4.0)
#> restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.4.0)
#> rintrojs 0.3.4 2024-01-11 [1] CRAN (R 4.4.0)
#> rjson 0.2.21 2022-01-09 [1] CRAN (R 4.4.0)
#> rlang 1.1.4 2024-06-04 [1] CRAN (R 4.4.0)
#> rmarkdown 2.27 2024-05-17 [1] CRAN (R 4.4.0)
#> Rsamtools 2.21.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> RSQLite 2.3.7 2024-05-27 [1] CRAN (R 4.4.0)
#> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0)
#> rtracklayer 1.65.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> S4Arrays 1.5.3 2024-07-03 [1] Bioconductor 3.20 (R 4.4.1)
#> S4Vectors 0.43.1 2024-07-03 [1] Bioconductor 3.20 (R 4.4.1)
#> sass 0.4.9 2024-03-15 [1] CRAN (R 4.4.0)
#> scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0)
#> scatterpie 0.2.3 2024-06-05 [1] CRAN (R 4.4.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
#> shadowtext 0.1.3 2024-01-19 [1] CRAN (R 4.4.0)
#> shape 1.4.6.1 2024-02-23 [1] CRAN (R 4.4.0)
#> shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.0)
#> shinyAce 0.4.2 2022-05-06 [1] CRAN (R 4.4.0)
#> shinycssloaders 1.0.0 2020-07-28 [1] CRAN (R 4.4.0)
#> shinyWidgets 0.8.6 2024-04-24 [1] CRAN (R 4.4.0)
#> SparseArray 1.5.17 2024-07-08 [1] Bioconductor 3.20 (R 4.4.1)
#> SparseM 1.84 2024-06-25 [1] CRAN (R 4.4.0)
#> stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0)
#> stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
#> SummarizedExperiment 1.35.1 2024-06-28 [1] Bioconductor 3.20 (R 4.4.1)
#> systemfonts 1.1.0 2024-05-15 [1] CRAN (R 4.4.0)
#> textshaping 0.4.0 2024-05-24 [1] CRAN (R 4.4.0)
#> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
#> tidygraph 1.3.1 2024-01-30 [1] CRAN (R 4.4.0)
#> tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.4.0)
#> tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
#> tidytree 0.4.6 2023-12-12 [1] CRAN (R 4.4.0)
#> tippy 0.1.0 2021-01-11 [1] CRAN (R 4.4.0)
#> topGO 2.57.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> treeio 1.29.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> tweenr 2.0.3 2024-02-26 [1] CRAN (R 4.4.0)
#> txdbmaker 1.1.1 2024-06-24 [1] Bioconductor 3.20 (R 4.4.1)
#> UCSC.utils 1.1.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0)
#> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
#> viridis 0.6.5 2024-01-29 [1] CRAN (R 4.4.0)
#> viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.4.0)
#> visNetwork 2.1.2 2022-09-29 [1] CRAN (R 4.4.0)
#> withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0)
#> xfun 0.45 2024-06-16 [1] CRAN (R 4.4.0)
#> XML 3.99-0.17 2024-06-25 [1] CRAN (R 4.4.0)
#> xml2 1.3.6 2023-12-04 [1] CRAN (R 4.4.0)
#> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0)
#> XVector 0.45.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> yaml 2.3.9 2024-07-05 [1] CRAN (R 4.4.0)
#> yulab.utils 0.1.4 2024-01-28 [1] CRAN (R 4.4.0)
#> zlibbioc 1.51.1 2024-06-05 [1] Bioconductor 3.20 (R 4.4.0)
#>
#> [1] /Users/runner/work/_temp/Library
#> [2] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
sessioninfo_extra()
#> Writing session info to file /var/folders/h9/l1shxhdd69nct08ylzq0n6q00000gn/T//RtmpWtWiKR/sessioninfoextra___file29b143f1b00d.txt
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.1 (2024-06-14)
#> os macOS Sonoma 14.5
#> system aarch64, darwin20
#> ui X11
#> language en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz UTC
#> date 2024-07-10
#> pandoc 3.1.11 @ /usr/local/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> abind 1.4-5 2016-07-21 [1] CRAN (R 4.4.0)
#> AnnotationDbi 1.67.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> ape 5.8 2024-04-11 [1] CRAN (R 4.4.0)
#> aplot 0.2.3 2024-06-17 [1] CRAN (R 4.4.0)
#> backbone 2.1.4 2024-05-09 [1] CRAN (R 4.4.0)
#> BiasedUrn 2.0.12 2024-06-16 [1] CRAN (R 4.4.0)
#> Biobase 2.65.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> BiocFileCache 2.13.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> BiocGenerics 0.51.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> BiocIO 1.15.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> BiocParallel 1.39.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> biomaRt 2.61.2 2024-06-24 [1] Bioconductor 3.20 (R 4.4.1)
#> Biostrings 2.73.1 2024-06-02 [1] Bioconductor 3.20 (R 4.4.0)
#> bit 4.0.5 2022-11-15 [1] CRAN (R 4.4.0)
#> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.4.0)
#> bitops 1.0-7 2021-04-24 [1] CRAN (R 4.4.0)
#> BIUMmisc * 0.2.0 2024-07-10 [1] local
#> blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.0)
#> bs4Dash 2.3.3 2024-01-23 [1] CRAN (R 4.4.0)
#> bslib 0.7.0 2024-03-29 [1] CRAN (R 4.4.0)
#> cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0)
#> circlize 0.4.16 2024-02-20 [1] CRAN (R 4.4.0)
#> cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.0)
#> clue 0.3-65 2023-09-23 [1] CRAN (R 4.4.0)
#> cluster 2.1.6 2023-12-01 [2] CRAN (R 4.4.1)
#> clusterProfiler 4.13.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> codetools 0.2-20 2024-03-31 [2] CRAN (R 4.4.1)
#> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.4.0)
#> colourpicker 1.3.0 2023-08-21 [1] CRAN (R 4.4.0)
#> ComplexHeatmap 2.21.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> ComplexUpset 1.3.3 2021-12-11 [1] CRAN (R 4.4.0)
#> cowplot 1.1.3 2024-01-22 [1] CRAN (R 4.4.0)
#> crayon 1.5.3 2024-06-20 [1] CRAN (R 4.4.0)
#> curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.0)
#> data.table 1.15.4 2024-03-30 [1] CRAN (R 4.4.0)
#> DBI 1.2.3 2024-06-02 [1] CRAN (R 4.4.0)
#> dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.4.0)
#> DelayedArray 0.31.6 2024-07-05 [1] Bioconductor 3.20 (R 4.4.1)
#> dendextend 1.17.1 2023-03-25 [1] CRAN (R 4.4.0)
#> desc 1.4.3 2023-12-10 [1] CRAN (R 4.4.0)
#> DESeq2 1.45.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> digest 0.6.36 2024-06-23 [1] CRAN (R 4.4.0)
#> doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.4.0)
#> DOSE 3.31.2 2024-06-14 [1] Bioconductor 3.20 (R 4.4.1)
#> dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.4.0)
#> DT 0.33 2024-04-04 [1] CRAN (R 4.4.0)
#> dynamicTreeCut 1.63-1 2016-03-11 [1] CRAN (R 4.4.0)
#> enrichplot 1.25.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> evaluate 0.24.0 2024-06-10 [1] CRAN (R 4.4.0)
#> expm 0.999-9 2024-01-11 [1] CRAN (R 4.4.0)
#> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0)
#> farver 2.1.2 2024-05-13 [1] CRAN (R 4.4.0)
#> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
#> fastmatch 1.1-4 2023-08-18 [1] CRAN (R 4.4.0)
#> fgsea 1.31.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> filelock 1.0.3 2023-12-11 [1] CRAN (R 4.4.0)
#> foreach 1.5.2 2022-02-02 [1] CRAN (R 4.4.0)
#> fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0)
#> geneLenDataBase 1.41.2 2024-06-13 [1] Bioconductor 3.20 (R 4.4.1)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0)
#> GeneTonic 2.9.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> GenomeInfoDb 1.41.1 2024-06-12 [1] Bioconductor 3.20 (R 4.4.1)
#> GenomeInfoDbData 1.2.12 2024-07-10 [1] Bioconductor
#> GenomicAlignments 1.41.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> GenomicFeatures 1.57.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> GenomicRanges 1.57.1 2024-06-12 [1] Bioconductor 3.20 (R 4.4.1)
#> GetoptLong 1.0.5 2020-12-15 [1] CRAN (R 4.4.0)
#> ggforce 0.4.2 2024-02-19 [1] CRAN (R 4.4.0)
#> ggfun 0.1.5 2024-05-28 [1] CRAN (R 4.4.0)
#> ggplot2 3.5.1 2024-04-23 [1] CRAN (R 4.4.0)
#> ggplotify 0.1.2 2023-08-09 [1] CRAN (R 4.4.0)
#> ggraph 2.2.1 2024-03-07 [1] CRAN (R 4.4.0)
#> ggrepel 0.9.5 2024-01-10 [1] CRAN (R 4.4.0)
#> ggridges 0.5.6 2024-01-23 [1] CRAN (R 4.4.0)
#> ggtree 3.13.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.4.0)
#> glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0)
#> GO.db 3.19.1 2024-07-10 [1] Bioconductor
#> GOSemSim 2.31.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> goseq 1.57.2 2024-06-12 [1] Bioconductor 3.20 (R 4.4.1)
#> graph 1.83.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> graphlayouts 1.1.1 2024-03-09 [1] CRAN (R 4.4.0)
#> gridExtra 2.3 2017-09-09 [1] CRAN (R 4.4.0)
#> gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.4.0)
#> gson 0.1.0 2023-03-07 [1] CRAN (R 4.4.0)
#> gtable 0.3.5 2024-04-22 [1] CRAN (R 4.4.0)
#> HDO.db 0.99.1 2024-07-10 [1] Bioconductor
#> hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
#> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#> htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0)
#> httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0)
#> httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0)
#> httr2 1.0.1 2024-04-01 [1] CRAN (R 4.4.0)
#> igraph 2.0.3 2024-03-13 [1] CRAN (R 4.4.0)
#> IRanges 2.39.1 2024-07-03 [1] Bioconductor 3.20 (R 4.4.1)
#> iterators 1.0.14 2022-02-05 [1] CRAN (R 4.4.0)
#> jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.4.0)
#> jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.4.0)
#> KEGGREST 1.45.1 2024-06-18 [1] Bioconductor 3.20 (R 4.4.1)
#> knitr 1.48 2024-07-07 [1] CRAN (R 4.4.0)
#> later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0)
#> lattice 0.22-6 2024-03-20 [2] CRAN (R 4.4.1)
#> lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.4.0)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
#> locfit 1.5-9.10 2024-06-24 [1] CRAN (R 4.4.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
#> MASS 7.3-61 2024-06-13 [1] CRAN (R 4.4.0)
#> Matrix 1.7-0 2024-04-26 [2] CRAN (R 4.4.1)
#> MatrixGenerics 1.17.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> matrixStats 1.3.0 2024-04-11 [1] CRAN (R 4.4.0)
#> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0)
#> mgcv 1.9-1 2023-12-21 [2] CRAN (R 4.4.1)
#> mime 0.12 2021-09-28 [1] CRAN (R 4.4.0)
#> miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0)
#> mosdef 1.1.0 2024-06-05 [1] Bioconductor 3.20 (R 4.4.0)
#> munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.0)
#> nlme 3.1-165 2024-06-06 [1] CRAN (R 4.4.0)
#> patchwork 1.2.0 2024-01-08 [1] CRAN (R 4.4.0)
#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
#> pkgdown 2.1.0.9000 2024-07-10 [1] Github (r-lib/pkgdown@f20a649)
#> plotly 4.10.4 2024-01-13 [1] CRAN (R 4.4.0)
#> plyr 1.8.9 2023-10-02 [1] CRAN (R 4.4.0)
#> png 0.1-8 2022-11-29 [1] CRAN (R 4.4.0)
#> polyclip 1.10-6 2023-09-27 [1] CRAN (R 4.4.0)
#> prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.4.0)
#> progress 1.2.3 2023-12-06 [1] CRAN (R 4.4.0)
#> promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0)
#> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0)
#> qvalue 2.37.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0)
#> ragg 1.3.2 2024-05-15 [1] CRAN (R 4.4.0)
#> rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.4.0)
#> RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.4.0)
#> Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.4.0)
#> RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.4.0)
#> reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.4.0)
#> restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.4.0)
#> rintrojs 0.3.4 2024-01-11 [1] CRAN (R 4.4.0)
#> rjson 0.2.21 2022-01-09 [1] CRAN (R 4.4.0)
#> rlang 1.1.4 2024-06-04 [1] CRAN (R 4.4.0)
#> rmarkdown 2.27 2024-05-17 [1] CRAN (R 4.4.0)
#> Rsamtools 2.21.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> RSQLite 2.3.7 2024-05-27 [1] CRAN (R 4.4.0)
#> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0)
#> rtracklayer 1.65.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> S4Arrays 1.5.3 2024-07-03 [1] Bioconductor 3.20 (R 4.4.1)
#> S4Vectors 0.43.1 2024-07-03 [1] Bioconductor 3.20 (R 4.4.1)
#> sass 0.4.9 2024-03-15 [1] CRAN (R 4.4.0)
#> scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0)
#> scatterpie 0.2.3 2024-06-05 [1] CRAN (R 4.4.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
#> shadowtext 0.1.3 2024-01-19 [1] CRAN (R 4.4.0)
#> shape 1.4.6.1 2024-02-23 [1] CRAN (R 4.4.0)
#> shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.0)
#> shinyAce 0.4.2 2022-05-06 [1] CRAN (R 4.4.0)
#> shinycssloaders 1.0.0 2020-07-28 [1] CRAN (R 4.4.0)
#> shinyWidgets 0.8.6 2024-04-24 [1] CRAN (R 4.4.0)
#> SparseArray 1.5.17 2024-07-08 [1] Bioconductor 3.20 (R 4.4.1)
#> SparseM 1.84 2024-06-25 [1] CRAN (R 4.4.0)
#> stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0)
#> stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
#> SummarizedExperiment 1.35.1 2024-06-28 [1] Bioconductor 3.20 (R 4.4.1)
#> systemfonts 1.1.0 2024-05-15 [1] CRAN (R 4.4.0)
#> textshaping 0.4.0 2024-05-24 [1] CRAN (R 4.4.0)
#> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
#> tidygraph 1.3.1 2024-01-30 [1] CRAN (R 4.4.0)
#> tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.4.0)
#> tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
#> tidytree 0.4.6 2023-12-12 [1] CRAN (R 4.4.0)
#> tippy 0.1.0 2021-01-11 [1] CRAN (R 4.4.0)
#> topGO 2.57.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> treeio 1.29.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> tweenr 2.0.3 2024-02-26 [1] CRAN (R 4.4.0)
#> txdbmaker 1.1.1 2024-06-24 [1] Bioconductor 3.20 (R 4.4.1)
#> UCSC.utils 1.1.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0)
#> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
#> viridis 0.6.5 2024-01-29 [1] CRAN (R 4.4.0)
#> viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.4.0)
#> visNetwork 2.1.2 2022-09-29 [1] CRAN (R 4.4.0)
#> withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0)
#> xfun 0.45 2024-06-16 [1] CRAN (R 4.4.0)
#> XML 3.99-0.17 2024-06-25 [1] CRAN (R 4.4.0)
#> xml2 1.3.6 2023-12-04 [1] CRAN (R 4.4.0)
#> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0)
#> XVector 0.45.0 2024-05-04 [1] Bioconductor 3.20 (R 4.4.0)
#> yaml 2.3.9 2024-07-05 [1] CRAN (R 4.4.0)
#> yulab.utils 0.1.4 2024-01-28 [1] CRAN (R 4.4.0)
#> zlibbioc 1.51.1 2024-06-05 [1] Bioconductor 3.20 (R 4.4.0)
#>
#> [1] /Users/runner/work/_temp/Library
#> [2] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────