# Detection of miRNAs that regulate interacting groups of pathways

## Documentation for package ‘PanomiR’ version 1.11.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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 k (depending on methodology) against a random distribution with jack-knifing of the pathway cluster (removing a pathway at a time)
linColumnFinder | Function imported from https://github.com/th1vairam/CovariateAnalysis Modified from http://stackoverflow.com/questions/13088770/ Function to find linearly dependednt columns of a matrix
mappingPathwaysClusters | Outputs a table with pathways and their respective clusters
methodProbBase | Outputs a table with col x, miRNA, probability of observing k against a random distribution of the cover of methodology
miniTestsPanomiR | Readouts and datasets for minimal reproducible examples of the PanomiR.
miRNAPathwayEnrichment | Enrichment Probability Of miRNAs
msigdb_c2 | Canonical pathways from Molecular Signatures Database, MsigDb V6.2
pathwayGeneTab | Pathway-Gene Associations
pathwaySummary | Pathway Summary Statistics
path_gene_table | A table of gene-pathway association. based on the pathways of MSigDB.
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 samples)
tableFromGSC | Pathway-Gene Associations from GeneSet collections
targetScan_03 | A processed list of miRNA target gene sets from the TargetScan dataset. Each list item is a list of genes targeted by the respective miRNA family