R version 4.2.1 (2022-06-23) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS Matrix products: default BLAS/LAPACK: /opt/miniconda3/envs/utap/lib/libopenblasp-r0.3.21.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 grid tools stats graphics grDevices utils [8] datasets methods base other attached packages: [1] knitr_1.40 [2] png_0.1-7 [3] heatmaply_1.3.0 [4] viridis_0.6.2 [5] viridisLite_0.4.1 [6] plotly_4.10.0 [7] DT_0.24 [8] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [9] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 [10] GenomicFeatures_1.48.3 [11] AnnotationDbi_1.58.0 [12] ChIPseeker_1.32.0 [13] openxlsx_4.2.5 [14] sva_3.44.0 [15] BiocParallel_1.30.3 [16] genefilter_1.78.0 [17] mgcv_1.8-40 [18] nlme_3.1-159 [19] fdrtool_1.2.17 [20] stringr_1.4.1 [21] reshape2_1.4.4 [22] tidyr_1.2.0 [23] dplyr_1.0.9 [24] plyr_1.8.7 [25] magrittr_2.0.3 [26] amap_0.8-18 [27] DESeq2_1.36.0 [28] SummarizedExperiment_1.26.1 [29] Biobase_2.56.0 [30] MatrixGenerics_1.8.1 [31] matrixStats_0.62.0 [32] GenomicRanges_1.48.0 [33] GenomeInfoDb_1.32.3 [34] IRanges_2.30.1 [35] S4Vectors_0.34.0 [36] BiocGenerics_0.42.0 [37] hexbin_1.28.2 [38] Glimma_2.6.0 [39] limma_3.52.2 [40] gridExtra_2.3 [41] ggdendro_0.1.23 [42] ggplot2_3.3.6 [43] gplots_3.1.3 [44] RColorBrewer_1.1-3 loaded via a namespace (and not attached): [1] utf8_1.2.2 tidyselect_1.1.2 RSQLite_2.2.16 [4] htmlwidgets_1.5.4 TSP_1.2-1 scatterpie_0.1.7 [7] munsell_0.5.0 codetools_0.2-18 withr_2.5.0 [10] colorspace_2.0-3 GOSemSim_2.22.0 filelock_1.0.2 [13] highr_0.9 DOSE_3.22.0 labeling_0.4.2 [16] GenomeInfoDbData_1.2.8 polyclip_1.10-0 bit64_4.0.5 [19] farver_2.1.1 vctrs_0.4.1 treeio_1.20.2 [22] generics_0.1.3 xfun_0.32 BiocFileCache_2.4.0 [25] R6_2.5.1 graphlayouts_0.8.1 seriation_1.3.6 [28] locfit_1.5-9.6 bitops_1.0-7 cachem_1.0.6 [31] fgsea_1.22.0 gridGraphics_0.5-1 DelayedArray_0.22.0 [34] assertthat_0.2.1 BiocIO_1.6.0 scales_1.2.1 [37] ggraph_2.0.6 enrichplot_1.16.1 gtable_0.3.0 [40] tidygraph_1.2.2 rlang_1.0.4 splines_4.2.1 [43] rtracklayer_1.56.1 lazyeval_0.2.2 yaml_2.3.5 [46] crosstalk_1.2.0 qvalue_2.28.0 ggplotify_0.1.0 [49] ellipsis_0.3.2 jquerylib_0.1.4 Rcpp_1.0.9 [52] progress_1.2.2 zlibbioc_1.42.0 purrr_0.3.4 [55] RCurl_1.98-1.8 prettyunits_1.1.1 ggrepel_0.9.1 [58] data.table_1.14.2 DO.db_2.9 hms_1.1.2 [61] patchwork_1.1.2 evaluate_0.16 xtable_1.8-4 [64] XML_3.99-0.10 compiler_4.2.1 biomaRt_2.52.0 [67] tibble_3.1.8 KernSmooth_2.23-20 crayon_1.5.1 [70] shadowtext_0.1.2 htmltools_0.5.3 ggfun_0.0.6 [73] geneplotter_1.74.0 aplot_0.1.6 DBI_1.1.3 [76] tweenr_2.0.1 dbplyr_2.2.1 MASS_7.3-58.1 [79] rappdirs_0.3.3 boot_1.3-28 Matrix_1.4-1 [82] cli_3.3.0 parallel_4.2.1 igraph_1.3.4 [85] pkgconfig_2.0.3 registry_0.5-1 GenomicAlignments_1.32.1 [88] xml2_1.3.3 foreach_1.5.2 ggtree_3.4.2 [91] annotate_1.74.0 bslib_0.4.0 webshot_0.5.5 [94] XVector_0.36.0 yulab.utils_0.0.5 digest_0.6.29 [97] Biostrings_2.64.1 rmarkdown_2.16 fastmatch_1.1-3 [100] tidytree_0.4.0 dendextend_1.16.0 edgeR_3.38.4 [103] restfulr_0.0.15 curl_4.3.2 Rsamtools_2.12.0 [106] gtools_3.9.3 rjson_0.2.21 lifecycle_1.0.1 [109] jsonlite_1.8.0 fansi_1.0.3 pillar_1.8.1 [112] lattice_0.20-45 KEGGREST_1.36.3 fastmap_1.1.0 [115] httr_1.4.4 plotrix_3.8-2 survival_3.4-0 [118] GO.db_3.15.0 glue_1.6.2 zip_2.2.0 [121] iterators_1.0.14 bit_4.0.4 ggforce_0.3.4 [124] stringi_1.7.8 sass_0.4.2 blob_1.2.3 [127] caTools_1.18.2 memoise_2.0.1 ape_5.6-2