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requirements.txt
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R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.9 (Green Obsidian)
Matrix products: default
BLAS: /cm/shared/apps/R4.0.3/lib64/R/lib/libRblas.so
LAPACK: /cm/shared/apps/R4.0.3/lib64/R/lib/libRlapack.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=de_DE.UTF-8 LC_MESSAGES=en_US.utf-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 grid stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] genesorteR_0.4.3 DoubletFinder_2.0.3
[3] Rmagic_2.0.3 SoupX_1.5.0
[5] celda_1.6.1 doParallel_1.0.16
[7] iterators_1.0.13 foreach_1.5.1
[9] data.table_1.14.0 Matrix_1.3-2
[11] future.apply_1.7.0 future_1.21.0
[13] progeny_1.12.0 futile.logger_1.4.3
[15] optparse_1.6.6 msigdbr_7.2.1
[17] ReactomePA_1.34.0 org.Hs.eg.db_3.12.0
[19] org.Mm.eg.db_3.12.0 clusterProfiler_3.18.1
[21] GSEABase_1.52.1 graph_1.68.0
[23] annotate_1.68.0 XML_3.99-0.6
[25] AnnotationDbi_1.52.0 scHCL_0.1.1
[27] scMCA_0.2.0 archive_1.1.0
[29] Nebulosa_1.0.2 patchwork_1.1.1
[31] schex_1.4.0 shiny_1.6.0
[33] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
[35] Biobase_2.50.0 GenomicRanges_1.42.0
[37] GenomeInfoDb_1.26.7 IRanges_2.24.1
[39] S4Vectors_0.28.1 BiocGenerics_0.36.0
[41] MatrixGenerics_1.2.1 matrixStats_0.58.0
[43] DOSE_3.16.0 plotly_4.9.3
[45] digest_0.6.27 WriteXLS_6.3.0
[47] gridExtra_2.3 ggsci_2.9
[49] ggridges_0.5.3 EnhancedVolcano_1.8.0
[51] ggrepel_0.9.1 ComplexHeatmap_2.6.2
[53] openxlsx_4.2.3 stringr_1.4.0
[55] clustree_0.4.3 ggraph_2.0.5
[57] urltools_1.7.3 reshape2_1.4.4
[59] cowplot_1.1.1 dplyr_1.0.5
[61] kableExtra_1.3.4 knitr_1.31
[63] Hmisc_4.5-0 ggplot2_3.3.3
[65] Formula_1.2-4 survival_3.2-7
[67] lattice_0.20-41 glue_1.4.2
[69] crayon_1.4.1 SeuratObject_4.0.0
[71] Seurat_4.0.1
loaded via a namespace (and not attached):
[1] ica_1.0-2 svglite_2.0.0
[3] assertive.properties_0.0-4 lmtest_0.9-38
[5] spatstat.core_2.1-2 MASS_7.3-53
[7] MAST_1.16.0 nlme_3.1-149
[9] backports_1.2.1 GOSemSim_2.16.1
[11] rlang_0.4.10 XVector_0.30.0
[13] ROCR_1.0-11 irlba_2.3.3
[15] extrafontdb_1.0 extrafont_0.17
[17] BiocParallel_1.24.1 rjson_0.2.20
[19] bit64_4.0.5 pheatmap_1.0.12
[21] sctransform_0.3.2 vipor_0.4.5
[23] spatstat.sparse_2.0-0 spatstat.geom_2.3-2
[25] tidyselect_1.1.0 fitdistrplus_1.1-3
[27] tidyr_1.1.3 assertive.types_0.0-3
[29] zoo_1.8-9 proj4_1.0-10
[31] xtable_1.8-4 magrittr_2.0.1
[33] evaluate_0.14 zlibbioc_1.36.0
[35] rstudioapi_0.13 miniUI_0.1.1.1
[37] rpart_4.1-15 fastmatch_1.1-0
[39] lambda.r_1.2.4 RcppEigen_0.3.3.9.1
[41] maps_3.3.0 xfun_0.22
[43] clue_0.3-58 cluster_2.1.0
[45] tidygraph_1.2.0 tibble_3.1.0
[47] listenv_0.8.0 png_0.1-7
[49] withr_2.4.1 bitops_1.0-6
[51] ggforce_0.3.3 plyr_1.8.6
[53] assertive.base_0.0-9 pracma_2.3.3
[55] pillar_1.5.1 GlobalOptions_0.1.2
[57] cachem_1.0.4 GetoptLong_1.0.5
[59] graphite_1.36.0 vctrs_0.3.7
[61] ellipsis_0.3.1 generics_0.1.0
[63] tools_4.0.3 foreign_0.8-80
[65] beeswarm_0.3.1 entropy_1.3.1
[67] munsell_0.5.0 tweenr_1.0.2
[69] fgsea_1.16.0 DelayedArray_0.16.3
[71] fastmap_1.1.0 compiler_4.0.3
[73] abind_1.4-5 httpuv_1.5.5
[75] GenomeInfoDbData_1.2.4 enrichR_3.0
[77] deldir_1.0-6 utf8_1.2.1
[79] later_1.1.0.1 jsonlite_1.7.2
[81] concaveman_1.1.0 multipanelfigure_2.1.2
[83] scales_1.1.1 pbapply_1.4-3
[85] lazyeval_0.2.2 promises_1.2.0.1
[87] latticeExtra_0.6-29 goftest_1.2-2
[89] spatstat.utils_2.3-0 reticulate_1.18
[91] checkmate_2.0.0 rmarkdown_2.7
[93] ash_1.0-15 webshot_0.5.2
[95] Rtsne_0.15 downloader_0.4
[97] uwot_0.1.10 igraph_1.2.6
[99] systemfonts_1.0.1 htmltools_0.5.1.1
[101] memoise_2.0.0 graphlayouts_0.7.1
[103] viridisLite_0.3.0 mime_0.10
[105] rappdirs_0.3.3 Rttf2pt1_1.3.8
[107] futile.options_1.0.1 RSQLite_2.2.6
[109] blob_1.2.1 shinythemes_1.2.0
[111] splines_4.0.3 Cairo_1.5-12.2
[113] RCurl_1.98-1.3 assertive.numbers_0.0-2
[115] ks_1.13.2 colorspace_2.0-0
[117] base64enc_0.1-3 BiocManager_1.30.12
[119] assertive.files_0.0-2 ggbeeswarm_0.6.0
[121] shape_1.4.5 ggrastr_0.2.3
[123] nnet_7.3-14 Rcpp_1.0.6
[125] mclust_5.4.7 RANN_2.6.1
[127] mvtnorm_1.1-1 circlize_0.4.12
[129] enrichplot_1.10.2 fansi_0.4.2
[131] parallelly_1.24.0 R6_2.5.0
[133] lifecycle_1.0.0 formatR_1.8
[135] zip_2.1.1 leiden_0.3.7
[137] getopt_1.20.3 DO.db_2.9
[139] qvalue_2.22.0 RcppAnnoy_0.0.18
[141] RColorBrewer_1.1-2 htmlwidgets_1.5.3
[143] polyclip_1.10-0 triebeard_0.3.0
[145] purrr_0.3.4 shadowtext_0.0.7
[147] gridGraphics_0.5-1 reactome.db_1.74.0
[149] rvest_1.0.0 mgcv_1.8-33
[151] globals_0.14.0 htmlTable_2.1.0
[153] codetools_0.2-16 GO.db_3.12.1
[155] MCMCprecision_0.4.0 gtable_0.3.0
[157] DBI_1.1.1 tensor_1.5
[159] httr_1.4.2 KernSmooth_2.23-17
[161] stringi_1.5.3 farver_2.1.0
[163] viridis_0.5.1 hexbin_1.28.2
[165] magick_2.7.1 DT_0.17
[167] xml2_1.3.2 combinat_0.0-8
[169] rvcheck_0.1.8 ggalt_0.4.0
[171] scattermore_0.7 bit_4.0.4
[173] scatterpie_0.1.5 jpeg_0.1-8.1
[175] spatstat.data_2.1-0 pkgconfig_2.0.3