All functions

collapseDataset

collapseDataset

CumulativeFractionPlot

Create Cumulative Fraction Plot.

DefineRegions

Define Regions Among Overlaps

DefineSignature

Defines a Signature based on Data Frame of Results

DESeqAnalysis

Automated Analysis of RNA-seq Data with Report Output (R Function)

ExpressionOverlapsTable

Table calculating overlaps of up to 3 tables

ggGeneset

Expression plot of genes within a geneset

ggGSEA

GSEA Plot via ggplot2 graphics

ggHighlights

Scatter plots with highlights for selected genesets.

ggSignaturePies

Signature Pie Chart Breakdown

ggVolcanos

Volcano Plots of Expression Data

multiplot

Multiple plot function

ngsAvgProf

Plotting function for ngs plots

peak2GRanges

Make venn diagram from GenomicRanges

ProcessIlluminaArray

Process Illumina Array

read.GMT

read.gmt

ReadCounts

Read Tag Counts over Regions Data

ReadHeatmaps

Read heatmap data from HOMER

ReadPeaks

Read in HOMER Peak files.

runGSEA.full

GSEA Wrapper Function

runGSEA

runGSEA This is an edited version of the GSEA function (GSEA 1.0), made to run directly in R. It does not provide all of the output that the GSEA algorithm provides, and there aren't any plots generated, but it will return p values and enrichment scores.

runLimma

runLimma

simpleCap

Simple Capitalization

SuperEnhancerPlot

Create a superEnhancer style plot

TranslateENSEMBL

Annotate ENSEMBL Gene IDs with Gene SYMBOL

TranslateKEGGIdentifiers

Translate KEGG ids to gene or ENSEMBL ids

TranslateKEGGPathway

Translate KEGG Pathway nodes KEGG IDs to gene SYMBOL or ENSEMBL

VennPeaks

Venn diagram data production from ReadPeaks

writeGMT

Write out a GMT File