Scripts for the analysis in simplifyEnrichment manuscript:
collect_sim_mat.R: It performes gene set enrichment analysis on EBI Expression Atlas datasets with various ontologies. It also calculates similarity matrices with different measurements on the significant terms.run_example_random_GO.R: It runs various clustering methods on the similarity matrices that were generated from random GO terms.run_examples_EBI.R: It runs various clustering methods on the similarity matrices from EBI Expression Atlas datasets.compare_semantic_and_overlap.R: It compares clusterings from different similarity measurements, i.e., semantic similarity and gene overlap similarities.test_partition_methods.R: It tests the effect of partitionning methods in the binary cut clustering with rando GO datasets.website.R: It deploys all the results to GitHub Page.figures/: Script for making figures in the manuscript.
Many analysis in the scripts were sent to the computing cluster with the bsub package.
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.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 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] gt_0.3.1 BiocManager_1.30.16 flexclust_1.4-0
[4] modeltools_0.2-23 lattice_0.20-44 reactome.db_1.76.0
[7] DO.db_2.9 AnnotationDbi_1.54.1 IRanges_2.26.0
[10] S4Vectors_0.30.0 Biobase_2.52.0 gridGraphics_0.5-1
[13] testthat_3.0.4 gridExtra_2.3 apcluster_1.4.8
[16] mclust_5.4.7 cowplot_1.1.1 ggplot2_3.3.5
[19] knitr_1.34 cola_1.99.4 msigdbr_7.4.1
[22] DOSE_3.18.2 dynamicTreeCut_1.63-1 dbscan_1.1-8
[25] MCL_1.0 igraph_1.2.6 clusterProfiler_4.2.0
[28] simplifyEnrichment_1.5.1 BiocGenerics_0.38.0 colorout_1.2-2
loaded via a namespace (and not attached):
[1] shadowtext_0.0.9 circlize_0.4.13 fastmatch_1.1-3
[4] plyr_1.8.6 lazyeval_0.2.2 proxyC_0.2.1
[7] splines_4.1.0 BiocParallel_1.26.2 GenomeInfoDb_1.28.4
[10] digest_0.6.27 htmltools_0.5.2 foreach_1.5.1
[13] yulab.utils_0.0.2 GOSemSim_2.18.1 viridis_0.6.1
[16] GO.db_3.13.0 fansi_0.5.0 magrittr_2.0.1
[19] memoise_2.0.0 tm_0.7-8 cluster_2.1.2
[22] doParallel_1.0.16 ComplexHeatmap_2.8.0 Biostrings_2.60.2
[25] graphlayouts_0.7.1 RcppParallel_5.1.4 matrixStats_0.61.0
[28] enrichplot_1.12.2 colorspace_2.0-2 blob_1.2.2
[31] ggrepel_0.9.1 xfun_0.24 dplyr_1.0.7
[34] microbenchmark_1.4-7 crayon_1.4.1 RCurl_1.98-1.5
[37] jsonlite_1.7.2 scatterpie_0.1.7 impute_1.66.0
[40] brew_1.0-6 iterators_1.0.13 ape_5.5
[43] glue_1.4.2 polyclip_1.10-0 gtable_0.3.0
[46] zlibbioc_1.38.0 XVector_0.32.0 GetoptLong_1.0.5
[49] shape_1.4.6 scales_1.1.1 DBI_1.1.1
[52] Rcpp_1.0.7 viridisLite_0.4.0 clue_0.3-59
[55] tidytree_0.3.5 bit_4.0.4 httr_1.4.2
[58] fgsea_1.18.0 RColorBrewer_1.1-2 ellipsis_0.3.2
[61] pkgconfig_2.0.3 farver_2.1.0 utf8_1.2.1
[64] ggplotify_0.1.0 tidyselect_1.1.1 rlang_0.4.12
[67] reshape2_1.4.4 munsell_0.5.0 tools_4.1.0
[70] cachem_1.0.5 downloader_0.4 generics_0.1.0
[73] RSQLite_2.2.8 stringr_1.4.0 fastmap_1.1.0
[76] ggtree_3.0.4 org.Hs.eg.db_3.13.0 babelgene_21.4
[79] bit64_4.0.5 tidygraph_1.2.0 purrr_0.3.4
[82] KEGGREST_1.32.0 ggraph_2.0.5 nlme_3.1-152
[85] slam_0.1-48 aplot_0.1.0 xml2_1.3.2
[88] compiler_4.1.0 rstudioapi_0.13 png_0.1-7
[91] treeio_1.16.2 tibble_3.1.4 tweenr_1.0.2
[94] stringi_1.7.4 Matrix_1.3-4 markdown_1.1
[97] vctrs_0.3.8 pillar_1.6.2 lifecycle_1.0.0
[100] eulerr_6.1.1 GlobalOptions_0.1.2 irlba_2.3.3
[103] data.table_1.14.0 bitops_1.0-7 patchwork_1.1.1
[106] qvalue_2.24.0 R6_2.5.1 codetools_0.2-18
[109] MASS_7.3-54 assertthat_0.2.1 rjson_0.2.20
[112] withr_2.4.2 GenomeInfoDbData_1.2.6 expm_0.999-6
[115] ggfun_0.0.4 class_7.3-19 tidyr_1.1.3
[118] skmeans_0.2-13 Cairo_1.5-12.2 ggforce_0.3.3
[121] NLP_0.2-1