Man pages for CBIIT-CGBB/OmicPath
OmicPath
| color_bar | generate color bar |
| db_names | get db names |
| do_GSEA | do GSEA |
| do_neighborhood | make networks by gene neighborhoods |
| ES | calculate enrichment score and p value |
| GO_hs | GO for human |
| GO_mm | GO mouse |
| GSEA.db | GSEA data object |
| hs2mm | convert human gene symbols to mouse |
| KEGG | KEGG |
| KEGG_mm | KEGG mouse |
| KEGGplot | KEGGplot |
| MGI_GenePheno_hs | MGI_GenePheno_hs |
| MGI_GenePheno_mm | MGI_GenePheno_mm |
| MGI_PhenoGenoMP_hs | MGI_PhenoGenoMP_hs |
| MGI_PhenoGenoMP_mm | MGI_PhenoGenoMP_mm |
| mm2hs | convert mouse gene symbols to human |
| MouseCyc | MouseCyc |
| msigdb.c1 | msigdb.c1 |
| msigdb.c2 | msigdb.c2 |
| msigdb.c2.cgp | msigdb.c2.cgp |
| msigdb.c2.cp.biocarta | msigdb.c2.cp.biocarta |
| msigdb.c2.cp.kegg | msigdb.c2.cp.kegg |
| msigdb.c2.cp.reactome | msigdb.c2.cp.reactome |
| msigdb.c3 | msigdb.c3 |
| msigdb.c3.mir | msigdb.c3.mir |
| msigdb.c3.tft | msigdb.c3.tft |
| msigdb.c4 | msigdb.c4 |
| msigdb.c4.cgn | msigdb.c4.cgn |
| msigdb.c4.cm | msigdb.c4.cm |
| msigdb.c5 | msigdb.c5 |
| msigdb.c5.bp | msigdb.c5.bp |
| msigdb.c5.cc | msigdb.c5.cc |
| msigdb.c6 | msigdb.c6 |
| msigdb.c7 | msigdb.c7 |
| msigdb.c8 | msigdb.c8 |
| msigdb.h | msigdb.h |
| msigdb.mm1.all | msigdb.mm1.all |
| msigdb.mm2.all | msigdb.mm2.all |
| msigdb.mm2.cgp | msigdb.mm2.cgp |
| msigdb.mm2.cp | msigdb.mm2.cp |
| msigdb.mm2.cp.biocarta | msigdb.mm2.cp.biocarta |
| msigdb.mm2.cp.reactome | msigdb.mm2.cp.reactome |
| msigdb.mm2.cp.wikipathways | msigdb.mm2.cp.wikipathways |
| msigdb.mm3.all | msigdb.mm3.all |
| msigdb.mm3.gtrd | msigdb.mm3.gtrd |
| msigdb.mm3.mirdb | msigdb.mm3.mirdb |
| msigdb.mm5.all | msigdb.mm5.all |
| msigdb.mm5.go | msigdb.mm5.go |
| msigdb.mm5.go.bp | msigdb.mm5.go.bp |
| msigdb.mm5.go.cc | msigdb.mm5.go.cc |
| msigdb.mm5.go.mf | msigdb.mm5.go.mf |
| msigdb.mm5.mpt | msigdb.mm5.mpt |
| msigdb.mm8.all | msigdb.mm8.all |
| msigdb.mmh.all | msigdb.mmh.all |
| NeST | NeST science.abf3067_table_s5.txt and GO |
| OmicPath | OmicPath package |
| pathway_append | pathway_append |
| pathway_creator | pathway_creator |
| pathway_delete | pathway_delete |
| pathway_search | pathway_search |
| pathway_update | pathway_update |
| PID_biocarta | PID_biocarta |
| PID_biocarta_mm | PID_biocarta mouse |
| PID_KEGG | PID_KEGG |
| PID_KEGG_mm | PID_KEGG mouse |
| PID_NCI_Nature_Curated | PID_NCI_Nature_Curated |
| PID_NCI_Nature_Curated_mm | PID_NCI_Nature_Curated mouse |
| plotKEGG | plotKEGG |
| plotNet | plotNet |
| ReactomePathways | ReactomePathways |
| similarity | do similarity |
| steiner_net | do steiner_net |
| WGCNA_6_1 | Step 1: checking data for WGCNA |
| WGCNA_6_2 | Step 2: estmating power value for WGCNA |
| WGCNA_6_3 | Step 3: determing module size for WGCNA |
| WGCNA_6_4 | Step 4: generating modules for WGCNA |
| WGCNA_6_5 | Step 5: generating network for WGCNA |
| WGCNA_6_6 | Step 6: GSEA for module for WGCNA |
| WGCNA_dissTOM | get dissTOM matrix |
| WGCNA_dissTOM2network | get network from dissTOM matrix |
