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checkIDmappingEfficiency()
|
Checks mapping efficiency for IDs on the most commonly used ID types |
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copy_bfabric_2grpGSEA()
|
copy all files needed to generate a bfabric report |
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copy_bfabric_ClusterProfiler()
|
copy all files needed to generate a bfabric report for cluster profiling |
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copy_gsea_report()
|
copy all files needed to generate GSEA report. |
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copy_multigroup_GSEA()
|
copy multigroup analysis |
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copy_ora_report()
|
copy all files needed to generate ORA report |
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cp_addurls_GO()
|
add uris to to cp table outputs |
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cp_clusterDPAEuclideanDist()
|
Cluster using DPA |
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cp_clusterHClustEuclideanDist()
|
cluster using hclust |
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cp_clusterHClustEuclideanDistDeepslit()
|
cluster using hclust and deepsplit |
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cp_compClust()
|
same as clusterProfiler::compareCluster but with defaults and error handling |
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cp_filterforNA()
|
remove proteins with more NA's than in 60% of samples |
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dist_JK()
|
JK resampling for dist function |
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DT_makeURLfor()
|
create url for data table |
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exampleContrastData
|
Contrast effect estimates |
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exampleUniprotIDs
|
Examplary Uniprot IDs |
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fgsea_leading_edge_too_char()
|
convert leading edge column to char for writing to file |
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fgsea_msigdb()
|
converts msigdb geneset to fgsea compatible |
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fgsea_msigdb_collections()
|
retrieve several msigdbr collections as fgsea compatible lists |
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fgsea_rank()
|
get fgsea compatible rank list from data.frame |
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fgsea_rank_contrasts()
|
convert data frame into list of ranks |
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getMsigdbGenesets()
|
getMsigdbGenesets |
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get_UniprotID_from_fasta_header()
|
Translate Fasta header to UniprotSwissprot ID |
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GPStab
|
Exemplary GPS table |
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GSEA
|
Exemplary GSEA output |
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GSEAex1
|
examplary GSEA output |
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makeGPS_wrappR()
|
makeGPS Wrapper
Function for generating background GPS repository for sigora and ora |
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mapthe()
|
helper function mapping clusters |
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map_ids_2ways()
|
map ids two ways |
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map_ids_annotationHub()
|
map id Annotation Hub |
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map_ids_uniprot()
|
map_ids_uniprot |
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myGPSrepo myGPSrepo
|
Examplary GPS repository |
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plotK()
|
plot cluster |
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runSIGORA()
|
workflow for sigORA |
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runWebGestaltGSEA()
|
workflow for GSEA |
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runWebGestaltORA()
|
workflow for ORA |
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run_fgsea_for_allContrasts()
|
run for all contrasts |
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run_fgsea_for_allGeneSets()
|
used to analyse a single contrast with various genesets |
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sigoraWrappR()
|
sigora Wrapper function |
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sigora_example
|
Exemplary sigora output |
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sigora_upsetR()
|
UpSetR wrapper for sigora results |