├── .Rbuildignore ├── .github └── workflows │ ├── conda_build.yml │ ├── helpers │ ├── call_tests.R │ └── mambabuild.yml │ └── r-beyondcell │ ├── build.sh │ ├── conda_build_config.yaml │ └── meta.yaml ├── .gitignore ├── .img ├── Logo_BU.png ├── beyondcell.png ├── drug_signatures.png ├── integrated_bendavid.png └── workflow_tutorial.png ├── CHANGELOG.md ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── .DS_Store ├── Basics.R ├── Format.R ├── Genesets.R ├── Manipulation.R ├── Ranks.R ├── Reductions.R ├── Score.R ├── Visualization.R ├── objects.R └── sysdata.rda ├── README.md ├── beyondcell.Rproj ├── data-raw ├── .DS_Store ├── CancerSEA │ ├── Angiogenesis.txt │ ├── Apoptosis.txt │ ├── Cell_Cycle.txt │ ├── DNA_damage.txt │ ├── DNA_repair.txt │ ├── Differentiation.txt │ ├── EMT.txt │ ├── Hypoxia.txt │ ├── Inflammation.txt │ ├── Invasion.txt │ ├── Metastasis.txt │ ├── Proliferation.txt │ ├── Quiescence.txt │ ├── README │ └── Stemness.txt ├── CreateTestData.R ├── Groger_2012 │ ├── GROGER_DN.txt │ ├── GROGER_UP.txt │ ├── REAME │ └── pone.0051136.s006.doc ├── Immunotherapy │ └── immunotherapy.gmt ├── MSigDB │ ├── ALONSO_METASTASIS_EMT_DN.txt │ ├── ALONSO_METASTASIS_EMT_UP.txt │ ├── FRIDMAN_SENESCENCE_DN.txt │ ├── FRIDMAN_SENESCENCE_UP.txt │ ├── GOBP_EPITHELIAL_TO_MESENCHYMAL_TRANSITION.txt │ ├── GOBP_NEGATIVE_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION.txt │ ├── GOBP_POSITIVE_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION.txt │ ├── GOBP_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION.txt │ ├── HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION.txt │ ├── HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN.txt │ ├── HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_UP.txt │ ├── HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_DN.txt │ ├── HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_UP.txt │ ├── REAME │ ├── WHITFIELD_CELL_CYCLE_G1_S.txt │ ├── WHITFIELD_CELL_CYCLE_G2.txt │ ├── WHITFIELD_CELL_CYCLE_G2_M.txt │ ├── WHITFIELD_CELL_CYCLE_LITERATURE.txt │ ├── WHITFIELD_CELL_CYCLE_M_G1.txt │ └── WHITFIELD_CELL_CYCLE_S.txt ├── PBMC3K_subset │ ├── barcodes.tsv │ ├── genes.tsv │ └── matrix.mtx ├── Visium │ ├── filtered_feature_bc_matrix.h5 │ ├── scalefactors_json.json │ ├── tissue_lowres_image.png │ └── tissue_positions_list.csv └── pathways.R ├── data ├── DSS.RData ├── PSc.RData ├── SSc.RData ├── drugInfo.RData └── immunotherapy.RData ├── man ├── .DS_Store ├── BreakString.Rd ├── CaseFraction.Rd ├── CreatebcObject.Rd ├── FindDrugs.Rd ├── GenerateGenesets.Rd ├── GetCollection.Rd ├── GetIDs.Rd ├── ListFilters.Rd ├── Mean.Med.SD.Rd ├── SwitchPoint.Rd ├── bc4Squares.Rd ├── bcAddMetadata.Rd ├── bcCellCycle.Rd ├── bcClusters.Rd ├── bcHistogram.Rd ├── bcMerge.Rd ├── bcRanks.Rd ├── bcRecompute.Rd ├── bcRegressOut.Rd ├── bcScore.Rd ├── bcSignatures.Rd ├── bcSubset.Rd ├── bcUMAP.Rd ├── beyondcell-class.Rd ├── center_scale_colour_stepsn.Rd ├── colMinus.Rd ├── geneset-class.Rd ├── get_colour_steps.Rd ├── minus.Rd ├── rankSigs.Rd └── readGMT.Rd ├── tests ├── testdata │ ├── gmt │ │ ├── correct10.gmt │ │ ├── correct100.gmt │ │ ├── correct10_names.txt │ │ ├── correct10down.gmt │ │ ├── correct10up.gmt │ │ ├── duplicated10.gmt │ │ ├── incorrect_mode10.gmt │ │ ├── score_warning10_nogenes.gmt │ │ ├── score_warning10_thres.gmt │ │ └── special_sigs.tsv │ ├── single-cell │ │ ├── barcodes.tsv │ │ ├── genes.tsv │ │ └── matrix.mtx │ └── visium │ │ ├── matrix.h5 │ │ ├── scalefactors_json.json │ │ ├── tissue_lowres_image.png │ │ └── tissue_positions_list.csv ├── testthat.R └── testthat │ ├── Rplots.pdf │ ├── test-GenerateGenesets.R │ ├── test-GetCollection.R │ ├── test-bcRegressOut.R │ ├── test-bcScore.R │ └── test-readGMT.R └── tutorial ├── BCS_normalization ├── .img │ ├── LFC-1.png │ ├── compareBCS-1.png │ ├── compareBCS-2.png │ ├── components_normalization-1.png │ ├── components_normalization-2.png │ ├── counts-1.png │ ├── rawBCS-1.png │ └── zeros-1.png └── README.md ├── ST_analysis ├── .img │ ├── TCs_and_pathologist.png │ ├── bc4squares_TC2.png │ └── lapatinib_ERBB2.png └── 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