Man pages for pouryany/PanomiR
Detection of miRNAs that regulate interacting groups of pathways
| aggInvCoverFn | Internal function for modification of prioritization. |
| aggInvFn | The function calculate targeting score of miRNA w.r.t to a... |
| aggLogCoverFn | Internal function for modification of prioritization. |
| aggLogFn | The function calculate targeting score of miRNA w.r.t to a... |
| alignToUniverse | function to align a list of sets and a reference universe |
| clusterPlot | Plots clusters of pathways with associated directionality. |
| differentialPathwayAnalysis | Differential Expression Analysis For Pathways |
| enrichAllPairs | Pairwise enrichment analysis between two given lists of sets |
| getDesignMatrix | Obtain Design Matrix |
| getDiffExpTable | function to get a DE table |
| getResidual | function to get residuals with respect to a set of covariates |
| gscExample | Example genesets from MSigDB |
| jackKnifeBase | Outputs a table with col x (miRNA), probability of observing... |
| linColumnFinder | Function imported from... |
| mappingPathwaysClusters | Outputs a table with pathways and their respective clusters |
| methodProbBase | Outputs a table with col x, miRNA, probability of observing k... |
| miniTestsPanomiR | Readouts and datasets for minimal reproducible examples of... |
| miRNAPathwayEnrichment | Enrichment Probability Of miRNAs |
| msigdb_c2 | Canonical pathways from Molecular Signatures Database, MsigDb... |
| path_gene_table | A table of gene-pathway association. based on the pathways of... |
| pathwayGeneTab | Pathway-Gene Associations |
| pathwaySummary | Pathway Summary Statistics |
| pCutCoverFn | Internal function for modification of prioritization. |
| pCutFn | Score miRNAs In a Cluster Of Pathways |
| pcxnToNet | Creates a network out of pcxn table |
| prioritizeMicroRNA | Prioritize miRNA |
| reportEnrichment | Publication-ready miRNA-Pathway Enrichment table |
| samplingDataBase | Outputs a table of sampling data(rows are miRNA and cols are... |
| sumlogCoverFn | Internal function for modification of prioritization. |
| sumlogFn | The function calculate targeting score of miRNA w.r.t to a... |
| sumzCoverFn | Internal function for modification of prioritization. |
| sumzFn | The function calculate targeting score of miRNA w.r.t to a... |
| tableFromGSC | Pathway-Gene Associations from GeneSet collections |
| targetScan_03 | A processed list of miRNA target gene sets from the... |
