Session Info
## R version 4.5.0 (2025-04-11)
## Platform: x86_64-pc-linux-gnu
## Running under: Red Hat Enterprise Linux 8.10 (Ootpa)
##
## Matrix products: default
## BLAS/LAPACK: FlexiBLAS OPENBLAS; LAPACK version 3.12.0
##
## Random number generation:
## RNG: L'Ecuyer-CMRG
## Normal: Inversion
## Sample: Rejection
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/Los_Angeles
## tzcode source: system (glibc)
##
## attached base packages:
## [1] parallel grid stats4 stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] org.Mm.eg.db_3.22.0 scater_1.38.0 scuttle_1.20.0
## [4] scRNAseq_2.24.0 dorothea_1.22.0 igraph_2.2.1
## [7] org.Hs.eg.db_3.22.0 nabor_0.5.0 msigdbr_25.1.1
## [10] epiregulon.extra_1.6.0 zellkonverter_1.20.0 ensembldb_2.34.0
## [13] AnnotationFilter_1.34.0 GenomicFeatures_1.62.0 AnnotationDbi_1.72.0
## [16] pbmcMultiome.SeuratData_0.1.4 SeuratData_0.2.2.9002 Signac_1.16.0
## [19] Seurat_5.3.1 SeuratObject_5.2.0 sp_2.2-0
## [22] epiregulon.archr_0.99.8 rhdf5_2.54.1 RcppArmadillo_15.2.2-1
## [25] Rcpp_1.1.0 sparseMatrixStats_1.22.0 data.table_1.17.8
## [28] stringr_1.6.0 plyr_1.8.9 magrittr_2.0.4
## [31] ggplot2_4.0.1 gtable_0.3.6 gtools_3.9.5
## [34] gridExtra_2.3 devtools_2.4.6 usethis_3.2.1
## [37] ArchR_1.0.3.1 Matrix_1.7-4 BSgenome.Hsapiens.UCSC.hg38_1.4.5
## [40] BSgenome_1.78.0 rtracklayer_1.70.0 BiocIO_1.20.0
## [43] Biostrings_2.78.0 XVector_0.50.0 GenomeInfoDb_1.46.2
## [46] epiregulon_2.0.2 scMultiome_1.10.0 SingleCellExperiment_1.32.0
## [49] MultiAssayExperiment_1.36.1 SummarizedExperiment_1.40.0 Biobase_2.70.0
## [52] GenomicRanges_1.62.0 Seqinfo_1.0.0 IRanges_2.44.0
## [55] S4Vectors_0.48.0 MatrixGenerics_1.22.0 matrixStats_1.5.0
## [58] ExperimentHub_3.0.0 AnnotationHub_4.0.0 BiocFileCache_3.0.0
## [61] dbplyr_2.5.1 BiocGenerics_0.56.0 generics_0.1.4
## [64] BiocStyle_2.38.0
##
## loaded via a namespace (and not attached):
## [1] graph_1.88.0 ica_1.0-3 plotly_4.11.0
## [4] BiocBaseUtils_1.12.0 doParallel_1.0.17 tidyselect_1.2.1
## [7] bit_4.6.0 clue_0.3-66 lattice_0.22-7
## [10] rjson_0.2.23 blob_1.2.4 S4Arrays_1.10.1
## [13] dichromat_2.0-0.1 seqLogo_1.76.0 png_0.1-8
## [16] cli_3.6.5 ggplotify_0.1.3 ProtGenerics_1.42.0
## [19] goftest_1.2-3 bluster_1.20.0 purrr_1.2.0
## [22] EnrichmentBrowser_2.40.0 BiocNeighbors_2.4.0 uwot_0.2.4
## [25] curl_7.0.0 mime_0.13 evaluate_1.0.5
## [28] tidytree_0.4.6 ComplexHeatmap_2.26.0 stringi_1.8.7
## [31] backports_1.5.0 XML_3.99-0.20 httpuv_1.6.16
## [34] clusterProfiler_4.18.2 rappdirs_0.3.3 splines_4.5.0
## [37] RcppRoll_0.3.1 ggraph_2.2.2 bcellViper_1.46.0
## [40] dplyr_1.1.4 sctransform_0.4.2 ggbeeswarm_0.7.3
## [43] sessioninfo_1.2.3 DBI_1.2.3 HDF5Array_1.38.0
## [46] jquerylib_0.1.4 withr_3.0.2 systemfonts_1.3.1
## [49] enrichplot_1.30.4 lmtest_0.9-40 ggnewscale_0.5.2
## [52] GSEABase_1.72.0 tidygraph_1.3.1 BiocManager_1.30.27
## [55] htmlwidgets_1.6.4 fs_1.6.6 ggrepel_0.9.6
## [58] labeling_0.4.3 SparseArray_1.10.6 h5mread_1.2.1
## [61] annotate_1.88.0 reticulate_1.44.1 zoo_1.8-14
## [64] knitr_1.50 TFBSTools_1.48.0 UCSC.utils_1.6.0
## [67] TFMPvalue_0.0.9 foreach_1.5.2 patchwork_1.3.2
## [70] caTools_1.18.3 ggtree_4.0.1 pwalign_1.6.0
## [73] R.oo_1.27.1 ggiraph_0.9.2 RSpectra_0.16-2
## [76] irlba_2.3.5.1 ggrastr_1.0.2 alabaster.schemas_1.10.0
## [79] fastDummies_1.7.5 gridGraphics_0.5-1 ellipsis_0.3.2
## [82] lazyeval_0.2.2 yaml_2.3.12 survival_3.8-3
## [85] scattermore_1.2 BiocVersion_3.22.0 crayon_1.5.3
## [88] RcppAnnoy_0.0.22 RColorBrewer_1.1-3 tidyr_1.3.1
## [91] progressr_0.18.0 tweenr_2.0.3 later_1.4.4
## [94] Rgraphviz_2.54.0 GlobalOptions_0.1.3 ggridges_0.5.7
## [97] codetools_0.2-20 KEGGREST_1.50.0 shape_1.4.6.1
## [100] Rtsne_0.17 limma_3.66.0 gdtools_0.4.4
## [103] Rsamtools_2.26.0 filelock_1.0.3 pkgconfig_2.0.3
## [106] KEGGgraph_1.70.0 spatstat.univar_3.1-5 GenomicAlignments_1.46.0
## [109] aplot_0.2.9 alabaster.base_1.10.0 spatstat.sparse_3.1-0
## [112] ape_5.8-1 viridisLite_0.4.2 xtable_1.8-4
## [115] httr_1.4.7 tools_4.5.0 globals_0.18.0
## [118] pkgbuild_1.4.8 beeswarm_0.4.0 checkmate_2.3.3
## [121] nlme_3.1-168 assertthat_0.2.1 digest_0.6.39
## [124] bookdown_0.46 dir.expiry_1.18.0 farver_2.1.2
## [127] reshape2_1.4.5 yulab.utils_0.2.2 viridis_0.6.5
## [130] DirichletMultinomial_1.52.0 glue_1.8.0 cachem_1.1.0
## [133] polyclip_1.10-7 parallelly_1.45.1 pkgload_1.4.1
## [136] statmod_1.5.1 RcppHNSW_0.6.0 ScaledMatrix_1.18.0
## [139] fontBitstreamVera_0.1.1 pbapply_1.7-4 httr2_1.2.2
## [142] spam_2.11-1 gson_0.1.0 dqrng_0.4.1
## [145] basilisk_1.22.0 graphlayouts_1.2.2 alabaster.se_1.10.0
## [148] shiny_1.12.1 tidydr_0.0.6 scrapper_1.4.0
## [151] R.utils_2.13.0 rhdf5filters_1.22.0 RCurl_1.98-1.17
## [154] alabaster.sce_1.10.0 memoise_2.0.1 rmarkdown_2.30
## [157] scales_1.4.0 R.methodsS3_1.8.2 gypsum_1.6.0
## [160] future_1.68.0 chromote_0.5.1 RANN_2.6.2
## [163] fontLiberation_0.1.0 Cairo_1.7-0 spatstat.data_3.1-9
## [166] rstudioapi_0.17.1 cluster_2.1.8.1 spatstat.utils_3.2-0
## [169] fitdistrplus_1.2-4 cowplot_1.2.0 colorspace_2.1-2
## [172] FNN_1.1.4.1 rlang_1.1.6 BSgenome.Hsapiens.UCSC.hg19_1.4.3
## [175] dotCall64_1.2 circlize_0.4.17 ggforce_0.5.0
## [178] ggtangle_0.0.9 xfun_0.54 alabaster.matrix_1.10.0
## [181] iterators_1.0.14 remotes_2.5.0 abind_1.4-8
## [184] GOSemSim_2.36.0 tibble_3.3.0 treeio_1.34.0
## [187] Rhdf5lib_1.32.0 motifmatchr_1.32.0 bitops_1.0-9
## [190] ps_1.9.1 promises_1.5.0 scatterpie_0.2.6
## [193] RSQLite_2.4.5 qvalue_2.42.0 fgsea_1.36.0
## [196] DelayedArray_0.36.0 GO.db_3.22.0 compiler_4.5.0
## [199] alabaster.ranges_1.10.0 beachmat_2.26.0 listenv_0.10.0
## [202] fontquiver_0.2.1 edgeR_4.8.0 BiocSingular_1.26.1
## [205] tensor_1.5.1 MASS_7.3-65 BiocParallel_1.44.0
## [208] babelgene_22.9 spatstat.random_3.4-3 R6_2.6.1
## [211] fastmap_1.2.0 fastmatch_1.1-6 vipor_0.4.7
## [214] ROCR_1.0-11 websocket_1.4.4 rsvd_1.0.5
## [217] KernSmooth_2.23-26 miniUI_0.1.2 deldir_2.0-4
## [220] htmltools_0.5.9 bit64_4.6.0-1 spatstat.explore_3.6-0
## [223] lifecycle_1.0.4 S7_0.2.1 processx_3.8.6
## [226] restfulr_0.0.16 sass_0.4.10 vctrs_0.6.5
## [229] rsconnect_1.7.0 spatstat.geom_3.6-1 DOSE_4.4.0
## [232] scran_1.38.0 ggfun_0.2.0 future.apply_1.20.1
## [235] bslib_0.9.0 pillar_1.11.1 magick_2.9.0
## [238] metapod_1.18.0 locfit_1.5-9.12 otel_0.2.0
## [241] jsonlite_2.0.0 GetoptLong_1.1.0 cigarillo_1.0.0