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 |