Files in protViz/prora
ORA, sigORA and GSEA functionalities for proteomic data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/DThelper.R
R/a_improtsFrom.R
R/addURLS.R
R/checkIDmappingEfficiency.R
R/cphelper.R
R/data.R
R/fgsea_utils.R
R/getUniprotFromFastaHeader.R
R/makeGPS_wrappR.R
R/makeSingleVisVariousEnrichments.R
R/make_ids_uniprot.R
R/msigDB_helper.R
R/runSigora.R
R/runWebGestalt.R
R/sigoraWrappR.R
R/utilities.R
R/vignetteHelpers.R
README.md
_pkgdown.yml
data/GPStab.rda
data/GSEA.rda
data/GSEAex1.rda
data/exampleContrastData.rda
data/exampleUniprotIDs.rda
data/myGPSrepo.rda
data/sigora_example.rda
inst/Hexsticker/cutProra.png
inst/Hexsticker/hexsticker.R
inst/Hexsticker/prora-1556186_1920.jpg
inst/Hexsticker/proraHex.png
inst/analyseMultiple2GrpOutputs/multigroupGSEA.Rmd
inst/analyseMultiple2GrpOutputs/prepare.R
inst/analyseSingle2GrpGSEA/.gitignore
inst/analyseSingle2GrpGSEA/ErrorMessage.Rmd
inst/analyseSingle2GrpGSEA/VisualizeSingle.Rmd
inst/analyseSingle2GrpGSEA/bFabricGSEAFrom2Grp.R
inst/analyseSingle2GrpGSEA/testReturnValues.R
inst/clusterProfiler/.gitignore
inst/clusterProfiler/WU268998.yaml
inst/clusterProfiler/WU269043.yaml
inst/clusterProfiler/WU269045.yaml
inst/clusterProfiler/analyseTSVwithArgs.R
inst/clusterProfiler/output_MaxQuant_info_WSpecies.csv
inst/clusterProfiler/profileClusters_V2.Rmd
inst/clusterProfiler/runscriptLocal.R
inst/fgcz_formatting/fgcz.css
inst/fgcz_formatting/fgcz_banner.png
inst/fgcz_formatting/fgcz_footer.html
inst/fgcz_formatting/fgcz_header.html
inst/rmarkdown_reports/.gitignore
inst/rmarkdown_reports/AbstractLS2.txt
inst/rmarkdown_reports/Figures/GO
inst/rmarkdown_reports/Figures/Table1.png
inst/rmarkdown_reports/Figures/Table1_n.png
inst/rmarkdown_reports/Figures/barchart.png
inst/rmarkdown_reports/Figures/enrichR.R
inst/rmarkdown_reports/Figures/enrichR.Rda
inst/rmarkdown_reports/Figures/getGeneSymbolsFromFastaHeader.R
inst/rmarkdown_reports/Figures/goslim_summary_Cells..p75...cmvto.png
inst/rmarkdown_reports/Figures/idMapping.R
inst/rmarkdown_reports/Figures/jobsummary.png
inst/rmarkdown_reports/Figures/sigora_simulation.R
inst/rmarkdown_reports/Figures/simulation_sigora.Rda
inst/rmarkdown_reports/Figures/webGestaltExample.rda
inst/rmarkdown_reports/Figures/wg_bar.svg
inst/rmarkdown_reports/GSEA.Rmd
inst/rmarkdown_reports/GSEA_Results_Overview.Rmd
inst/rmarkdown_reports/ORAGSEAcomparison.Rmd
inst/rmarkdown_reports/ORA_Results_Overview.Rmd
inst/rmarkdown_reports/bibliography.bib
inst/rmarkdown_reports/fgczgseaora_meeting.Rmd
inst/rmarkdown_reports/sigora.Rmd
inst/rmarkdown_reports/sigora_example.Rmd
inst/run_scripts/annotationHub.R
inst/run_scripts/lfq_2grp_sigora.R
inst/run_scripts/lfq_multigroup_gsea.R
inst/run_scripts/lfq_multigroup_ora.R
inst/run_scripts/mappingExampleCode.R
inst/sample/.gitignore
inst/sample/fgseavignette.Rmd
inst/sample/p3433_analyse.R
inst/sample/test_ggsea_Multi.Rmd
inst/sampleData/CanisLupus.xlsx
inst/sampleData/YEAST_Example.xlsx
inst/sigora_3.0.2.tar.gz
inst/win/lfq_2grp_webgestalt_gsea.bat
man/DT_makeURLfor.Rd
man/GPStab.Rd
man/GSEA.Rd
man/checkIDmappingEfficiency.Rd
man/copy_bfabric_2grpGSEA.Rd
man/copy_bfabric_ClusterProfiler.Rd
man/copy_gsea_report.Rd
man/copy_multigroup_GSEA.Rd
man/copy_ora_report.Rd
man/cp_addurls_GO.Rd
man/cp_clusterDPAEuclideanDist.Rd
man/cp_clusterHClustEuclideanDist.Rd
man/cp_clusterHClustEuclideanDistDeepslit.Rd
man/cp_compClust.Rd
man/cp_filterforNA.Rd
man/dist_JK.Rd
man/exampleContrastData.Rd
man/exampleUniprotIDs.Rd
man/fgsea_leading_edge_too_char.Rd
man/fgsea_msigdb.Rd
man/fgsea_msigdb_collections.Rd
man/fgsea_rank.Rd
man/fgsea_rank_contrasts.Rd
man/figures/cutProra.png
man/figures/proraHex.png
man/getMsigdbGenesets.Rd
man/get_UniprotID_from_fasta_header.Rd
man/makeGPS_wrappR.Rd
man/map_ids_2ways.Rd
man/map_ids_annotationHub.Rd
man/map_ids_uniprot.Rd
man/mapthe.Rd
man/myGPSrepo.Rd
man/plotK.Rd
man/runSIGORA.Rd
man/runWebGestaltGSEA.Rd
man/runWebGestaltORA.Rd
man/run_fgsea_for_allContrasts.Rd
man/run_fgsea_for_allGeneSets.Rd
man/sigoraWrappR.Rd
man/sigora_example.Rd
man/sigora_upsetR.Rd
prora.Rproj
tests/test_gsea.R
tests/test_sigora.R
tests/test_webgestalt_ora.R
vignettes/.gitignore
vignettes/bibliography.bib
vignettes/vignette.Rmd
