Detection of miRNAs that regulate interacting groups of pathways

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Documentation for package ‘PanomiR’ version 1.12.0

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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