Man pages for protViz/fgcz.gsea.ora
ORA, sigORA and GSEA functionalities for proteomic data

checkIDmappingEfficiencyChecks mapping efficiency for IDs on the most commonly used...
copy_bfabric_2grpGSEAcopy all files needed to generate a bfabric report
copy_bfabric_ClusterProfilercopy all files needed to generate a bfabric report for...
copy_gsea_reportcopy all files needed to generate GSEA report.
copy_multigroup_GSEAcopy multigroup analysis
copy_ora_reportcopy all files needed to generate ORA report
cp_addurls_GOadd uris to to cp table outputs
cp_clusterDPAEuclideanDistCluster using DPA
cp_clusterHClustEuclideanDistcluster using hclust
cp_clusterHClustEuclideanDistDeepslitcluster using hclust and deepsplit
cp_compClustsame as clusterProfiler::compareCluster but with defaults and...
cp_filterforNAremove proteins with more NA's than in 60% of samples
dist_JKJK resampling for dist function
DT_makeURLforcreate url for data table
exampleContrastDataContrast effect estimates
exampleUniprotIDsExamplary Uniprot IDs
fgsea_leading_edge_too_charconvert leading edge column to char for writing to file
fgsea_msigdbconverts msigdb geneset to fgsea compatible
fgsea_msigdb_collectionsretrieve several msigdbr collections as fgsea compatible...
fgsea_rankget fgsea compatible rank list from data.frame
fgsea_rank_contrastsconvert data frame into list of ranks
getMsigdbGenesetsgetMsigdbGenesets
get_UniprotID_from_fasta_headerTranslate Fasta header to UniprotSwissprot ID
GPStabExemplary GPS table
GSEAExemplary GSEA output
makeGPS_wrappRmakeGPS Wrapper Function for generating background GPS...
map_ids_2waysmap ids two ways
map_ids_annotationHubmap id Annotation Hub
map_ids_uniprotmap_ids_uniprot
mapthehelper function mapping clusters
myGPSrepoExamplary GPS repository
plotKplot cluster
run_fgsea_for_allContrastsrun for all contrasts
run_fgsea_for_allGeneSetsused to analyse a single contrast with various genesets
runSIGORAworkflow for sigORA
runWebGestaltGSEAworkflow for GSEA
runWebGestaltORAworkflow for ORA
sigora_exampleExemplary sigora output
sigora_upsetRUpSetR wrapper for sigora results
sigoraWrappRsigora Wrapper function
protViz/fgcz.gsea.ora documentation built on Dec. 24, 2021, 9:47 a.m.