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 |