Files in girke-lab/signatureSearch
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/AllClasses.R
R/AllGenerics.R
R/RcppExports.R
R/aa-global.R
R/accessor.R
R/build_custom_db.R
R/comp_fea_res.R
R/dsea_GSEA.R
R/dsea_hyperG.R
R/dtnetplot.R
R/feaResult-methods.R
R/fgsea2.R
R/gessResult-methods.R
R/gess_cmap.R
R/gess_cor.R
R/gess_fisher.R
R/gess_gcmap.R
R/gess_lincs.R
R/gess_res_summary.R
R/get_functional_catgory_data.R
R/get_targets.R
R/gseAnalyzer2.R
R/gsea_internal.R
R/gsea_internal2.R
R/io.R
R/mabsAnalyser.R
R/mabs_internal.R
R/moa_conn.R
R/oraAnalyzer.R
R/ora_internal.R
R/qSig-methods.R
R/refdb_treat_info.R
R/runWF.R
R/signatureSearch-package.r
R/sysdata.rda
R/tsea_dup_hyperG.R
R/tsea_mGSEA.R
R/tsea_mabs.R
R/utilities.R
README.md
data-raw/cell_info.R
data-raw/cell_info2.R
data-raw/chembl_moa_list.R
data-raw/clue_moa_list.R
data-raw/getPertInfo.R
data-raw/lincs_info.R
data-raw/lincs_pert_info.R
data-raw/lincs_pert_info2.R
data-raw/target_chembl2uniprotID.ipynb
data-raw/univ_go.R
data/cell_info.rda
data/cell_info2.rda
data/chembl_moa_list.rda
data/clue_moa_list.rda
data/drugs10.rda
data/lincs_expr_inst_info.rda
data/lincs_pert_info.rda
data/lincs_pert_info2.rda
data/lincs_sig_info.rda
data/targetList.rda
inst/CITATION
inst/extdata/GESS_FEA_report.Rmd
inst/extdata/GESS_report.Rmd
inst/extdata/LINCSGeneSpaceSub.txt
inst/extdata/sample_db.h5
inst/extdata/slurm.tmpl
inst/extdata/test_gene_sets_n4.gmt
inst/extdata/test_sample_n2x12328.gctx
man/GCT-object.Rd
man/addGESSannot.Rd
man/addMOA.Rd
man/add_pcid.Rd
man/append2H5.Rd
man/build_custom_db.Rd
man/calcGseaStatBatchCpp.Rd
man/cellNtestPlot.Rd
man/cell_info.Rd
man/cell_info2.Rd
man/chembl_moa_list.Rd
man/clue_moa_list.Rd
man/comp_fea_res.Rd
man/create_empty_h5.Rd
man/dim-methods.Rd
man/drug_cell_ranks.Rd
man/drugs-methods.Rd
man/drugs10.Rd
man/dtnetplot.Rd
man/enrichGO2.Rd
man/enrichKEGG2.Rd
man/enrichMOA.Rd
man/enrichReactome.Rd
man/fea.Rd
man/feaResult-class.Rd
man/feaResult.Rd
man/gctx2h5.Rd
man/gess.Rd
man/gessResult-class.Rd
man/gessResult.Rd
man/gess_res_vis.Rd
man/getALLEG.Rd
man/getDb.Rd
man/getSig.Rd
man/getTreats.Rd
man/get_targets.Rd
man/gmt2h5.Rd
man/gseGO2.Rd
man/gseKEGG2.Rd
man/gseReactome.Rd
man/head-methods.Rd
man/lincs_expr_inst_info.Rd
man/lincs_pert_info.Rd
man/lincs_pert_info2.Rd
man/lincs_sig_info.Rd
man/list2df.Rd
man/list_rev.Rd
man/mabsGO.Rd
man/mabsKEGG.Rd
man/mabsReactome.Rd
man/matrix2h5.Rd
man/meanExpr2h5.Rd
man/moa_conn.Rd
man/parse_gctx.Rd
man/qSig-class.Rd
man/qSig.Rd
man/rand_query_ES.Rd
man/read_gmt.Rd
man/result-methods.Rd
man/runWF.Rd
man/set_readable.Rd
man/show-methods.Rd
man/signatureSearch-package.Rd
man/sim_score_grp.Rd
man/tail-methods.Rd
man/tarReduce.Rd
man/targetList.Rd
man/vec_char_redu.Rd
src/RcppExports.cpp
src/fastGSEA.cpp
src/fastGSEA.h
src/fgsea_init.c
tests/testthat.R
vignettes/bibtex.bib
vignettes/images/lincs_cell_ntest.png
vignettes/images/ss_fc.png
vignettes/images/ss_wf.png
vignettes/images/vorinostat_SKB_lincs_gess_res_vis.png
vignettes/signatureSearch.Rmd
