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Table 2 List of Software Modules

From: Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis

Name

Goal

Full Pipelines

Pipeline_UnmappedReads.kar

Full pipeline starting with unmapped reads

Pipeline_MappedReads(.kar/.R)

Full pipeline starting with mapped reads

Pipeline_MappedReadsAndExternalPeakFile(.kar/.R)

Full pipeline starting with mapped reads and a file of peaks

Pipeline_onlyExternalPeakFile(.kar/.R)

Full pipeline when only file of peaks is available

Independent Modules

MapReads.kar

Map reads to a reference genome

AnnotatePeaks(.kar/.R)

Map peaks to genes

CalcDistanceToTSS(.kar/.R)

Summary of peak distance to TSS

CalcPeakStats(.kar/.R)

Summary peak statistics

GeneOntologyAnalysis(.kar/.R)

Gene Ontology Analysis

GeneratePeakExamples(.kar/.R)

Generate a set of graphs of peak and non-peak regions automatically

GetPeakSequences(.kar/.R)

Generate set of DNA sequences from peaks

MakeTSSHeatmapAndDensityPlots(.kar/.R)

Makes a heatmap of reads around all TSSs and also an average profile plot

MakeUCSCfile(.kar/.R)

Makes a bedgraph.tar.gz file ready for direct upload to the UCSC genome browser

MotifDiscovery(.kar/.R)

Runs MEME to attempt motif finding from peaks

PathwayAnalysis(.kar/.R)

Performs a pathway analysis, generates list of high-scoring pathways and images of results

RunMACS(.kar/.R)

Runs MACS to predict peaks

Utility

BamToBed(.kar/.R)

Converts bam format to bed format

IndexBAM(.kar/.R)

Indexes a bam file

SamToBed(.kar/.R)

Converts sam format to bed format

Extra

GraphSingleDataRange(.kar/.R)

Generates a graph of read density for any region of the genome

  1. Notes: (.kar/.R) refers to workflows having Kepler (.kar) and R (.R) versions. The same root name is used; for example RunMACS.kar and RunMACS.R