References¶

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Neo Christopher Chung, John D. Storey, Statistical significance of variables driving systematic variation in high-dimensional data, Bioinformatics, Volume 31, Issue 4, 15 February 2015, Pages 545–554, https://doi.org/10.1093/bioinformatics/btu674

Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, +7, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, Scott L. Pomeroy, Todd R. Golub, Eric S. Lander, and Jill P. Mesirov. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS, Volume 102, Number 43, Pages 15545-15550, (2005) https://doi.org/10.1073/pnas.0506580102

Mootha, V., Lindgren, C., Eriksson, KF. et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34, 267–273 (2003). https://doi.org/10.1038/ng1180

Arthur Liberzon, Aravind Subramanian, Reid Pinchback, Helga Thorvaldsdóttir, Pablo Tamayo, Jill P. Mesirov, Molecular signatures database (MSigDB) 3.0, Bioinformatics, Volume 27, Issue 12, 15 June 2011, Pages 1739–1740, https://doi.org/10.1093/bioinformatics/btr260

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sessionInfo()

## R version 4.1.0 (2021-05-18)
## Platform: x86_64-conda-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
##
## Matrix products: default
## BLAS/LAPACK: /opt/rstudio-server_conda/conda/envs/rstudio-server_4.1.0/lib/libopenblasp-r0.3.15.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] parallel  stats4    stats     graphics  grDevices utils     datasets
## [8] methods   base
##
## other attached packages:
##  [1] vroom_1.5.7           msigdbr_7.5.1         rmarkdown_2.14
##  [4] knitr_1.39            enrichplot_1.12.3     org.Hs.eg.db_3.13.0
##  [7] AnnotationDbi_1.54.1  IRanges_2.26.0        S4Vectors_0.30.2
## [10] Biobase_2.52.0        BiocGenerics_0.38.0   clusterProfiler_4.0.5
## [13] clustree_0.4.4        magrittr_2.0.3        dplyr_1.0.9
## [16] plyr_1.8.7            biomaRt_2.48.3        RColorBrewer_1.1-3
## [19] gridExtra_2.3         ggraph_2.0.5          ggplot2_3.3.6
## [22] sp_1.4-7              SeuratObject_4.1.0    Seurat_4.1.1
##
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.2             reticulate_1.22        tidyselect_1.1.2
##   [4] RSQLite_2.2.14         htmlwidgets_1.5.4      grid_4.1.0
##   [7] BiocParallel_1.26.2    Rtsne_0.16             scatterpie_0.1.7
##  [10] munsell_0.5.0          codetools_0.2-18       ica_1.0-2
##  [13] future_1.25.0          miniUI_0.1.1.1         withr_2.5.0
##  [16] spatstat.random_2.2-0  colorspace_2.0-3       GOSemSim_2.18.1
##  [19] progressr_0.10.1       filelock_1.0.2         highr_0.9
##  [22] rstudioapi_0.13        ROCR_1.0-11            tensor_1.5
##  [25] DOSE_3.18.3            listenv_0.8.0          labeling_0.4.2
##  [28] GenomeInfoDbData_1.2.6 polyclip_1.10-0        bit64_4.0.5
##  [31] farver_2.1.0           downloader_0.4         treeio_1.16.2
##  [34] parallelly_1.32.0      vctrs_0.4.1            generics_0.1.2
##  [37] xfun_0.31              BiocFileCache_2.0.0    R6_2.5.1
##  [40] GenomeInfoDb_1.28.4    graphlayouts_0.8.0     gridGraphics_0.5-1
##  [43] bitops_1.0-7           spatstat.utils_2.3-1   cachem_1.0.6
##  [46] fgsea_1.18.0           assertthat_0.2.1       promises_1.2.0.1
##  [49] scales_1.2.0           rgeos_0.5-9            gtable_0.3.0
##  [52] globals_0.15.0         goftest_1.2-3          tidygraph_1.2.1
##  [55] rlang_1.0.2            splines_4.1.0          lazyeval_0.2.2
##  [58] checkmate_2.1.0        spatstat.geom_2.4-0    yaml_2.3.5
##  [61] reshape2_1.4.4         abind_1.4-5            backports_1.4.1
##  [64] httpuv_1.6.5           qvalue_2.24.0          tools_4.1.0
##  [67] ggplotify_0.1.0        ellipsis_0.3.2         spatstat.core_2.4-4
##  [70] ggridges_0.5.3         Rcpp_1.0.8.3           progress_1.2.2
##  [73] zlibbioc_1.38.0        purrr_0.3.4            RCurl_1.98-1.6
##  [76] prettyunits_1.1.1      rpart_4.1.16           deldir_1.0-6
##  [79] pbapply_1.5-0          viridis_0.6.2          cowplot_1.1.1
##  [82] zoo_1.8-10             ggrepel_0.9.1          cluster_2.1.3
##  [85] RSpectra_0.16-1        data.table_1.14.2      scattermore_0.8
##  [88] DO.db_2.9              lmtest_0.9-40          RANN_2.6.1
##  [91] fitdistrplus_1.1-8     matrixStats_0.62.0     hms_1.1.1
##  [94] patchwork_1.1.1        mime_0.12              evaluate_0.15
##  [97] xtable_1.8-4           XML_3.99-0.9           compiler_4.1.0
## [100] tibble_3.1.7           shadowtext_0.1.2       KernSmooth_2.23-20
## [103] crayon_1.5.1           htmltools_0.5.2        tzdb_0.3.0
## [106] ggfun_0.0.6            mgcv_1.8-40            later_1.3.0
## [109] aplot_0.1.4            tidyr_1.2.0            DBI_1.1.2
## [112] tweenr_1.0.2           dbplyr_2.1.1           MASS_7.3-57
## [115] rappdirs_0.3.3         babelgene_22.3         Matrix_1.4-1
## [118] cli_3.3.0              igraph_1.3.1           pkgconfig_2.0.3
## [121] plotly_4.10.0          spatstat.sparse_2.1-1  xml2_1.3.3
## [124] ggtree_3.0.4           XVector_0.32.0         yulab.utils_0.0.4
## [127] stringr_1.4.0          digest_0.6.29          sctransform_0.3.3
## [130] RcppAnnoy_0.0.19       spatstat.data_2.2-0    Biostrings_2.60.2
## [133] leiden_0.4.2           fastmatch_1.1-3        tidytree_0.3.9
## [136] uwot_0.1.11            curl_4.3.2             shiny_1.7.1
## [139] lifecycle_1.0.1        nlme_3.1-157           jsonlite_1.8.0
## [142] limma_3.48.3           viridisLite_0.4.0      fansi_1.0.3
## [145] pillar_1.7.0           lattice_0.20-45        KEGGREST_1.32.0
## [148] fastmap_1.1.0          httr_1.4.3             survival_3.3-1
## [151] GO.db_3.13.0           glue_1.6.2             png_0.1-7
## [154] bit_4.0.4              ggforce_0.3.3          stringi_1.7.6
## [157] blob_1.2.3             memoise_2.0.1          ape_5.6-2
## [160] irlba_2.3.5            future.apply_1.9.0