Man pages for protViz/prora
ORA, sigORA and GSEA functionalities for proteomic data
| checkIDmappingEfficiency | Checks mapping efficiency for IDs on the most commonly used... |
| copy_bfabric_2grpGSEA | copy all files needed to generate a bfabric report |
| copy_bfabric_ClusterProfiler | copy all files needed to generate a bfabric report for... |
| copy_gsea_report | copy all files needed to generate GSEA report. |
| copy_multigroup_GSEA | copy multigroup analysis |
| copy_ora_report | copy all files needed to generate ORA report |
| cp_addurls_GO | add uris to to cp table outputs |
| cp_clusterDPAEuclideanDist | Cluster using DPA |
| cp_clusterHClustEuclideanDist | cluster using hclust |
| cp_clusterHClustEuclideanDistDeepslit | cluster using hclust and deepsplit |
| cp_compClust | same as clusterProfiler::compareCluster but with defaults and... |
| cp_filterforNA | remove proteins with more NA's than in 60% of samples |
| dist_JK | JK resampling for dist function |
| DT_makeURLfor | create url for data table |
| exampleContrastData | Contrast effect estimates |
| exampleUniprotIDs | Examplary Uniprot IDs |
| fgsea_leading_edge_too_char | convert leading edge column to char for writing to file |
| fgsea_msigdb | converts msigdb geneset to fgsea compatible |
| fgsea_msigdb_collections | retrieve several msigdbr collections as fgsea compatible... |
| fgsea_rank | get fgsea compatible rank list from data.frame |
| fgsea_rank_contrasts | convert data frame into list of ranks |
| getMsigdbGenesets | getMsigdbGenesets |
| get_UniprotID_from_fasta_header | Translate Fasta header to UniprotSwissprot ID |
| GPStab | Exemplary GPS table |
| GSEA | Exemplary GSEA output |
| makeGPS_wrappR | makeGPS Wrapper Function for generating background GPS... |
| map_ids_2ways | map ids two ways |
| map_ids_annotationHub | map id Annotation Hub |
| map_ids_uniprot | map_ids_uniprot |
| mapthe | helper function mapping clusters |
| myGPSrepo | Examplary GPS repository |
| plotK | plot cluster |
| run_fgsea_for_allContrasts | run for all contrasts |
| run_fgsea_for_allGeneSets | used to analyse a single contrast with various genesets |
| runSIGORA | workflow for sigORA |
| runWebGestaltGSEA | workflow for GSEA |
| runWebGestaltORA | workflow for ORA |
| sigora_example | Exemplary sigora output |
| sigora_upsetR | UpSetR wrapper for sigora results |
| sigoraWrappR | sigora Wrapper function |
