GitHub - nuprofessor/NGSbartom: NGS pipeline put together in collaboration with the Shilatifard lab at Northwestern University.

Name		Name	Last commit message	Last commit date
Latest commit History 9 Commits
FastQC		FastQC
MACS-1.4.2		MACS-1.4.2
SICER_V1.1/SICER		SICER_V1.1/SICER
Trimmomatic-0.33		Trimmomatic-0.33
bedtools2		bedtools2
bowtie-1.0.0		bowtie-1.0.0
fromAshley		fromAshley
java-genomics-toolkit		java-genomics-toolkit
samtools-0.1.19		samtools-0.1.19
.RData		.RData
.Rhistory		.Rhistory
addGenesToBed.R		addGenesToBed.R
bedGraphToBigWig		bedGraphToBigWig
bedToBigBed		bedToBigBed
bigWigToBedGraph		bigWigToBedGraph
buildPipelineScripts.pl		buildPipelineScripts.pl
createChIPtracks.R		createChIPtracks.R
createChIPtracks2.R		createChIPtracks2.R
createRNAcounts.R		createRNAcounts.R
createRNAcounts2.R		createRNAcounts2.R
createRNAseqTracks.R		createRNAseqTracks.R
createRNAseqTracks2.R		createRNAseqTracks2.R
createTophatReport.R		createTophatReport.R
findCorrelatedGenes.R		findCorrelatedGenes.R
fromBedPlusBWsToCDT.R		fromBedPlusBWsToCDT.R
fromBedPlusBWsToCDTnPlot.R		fromBedPlusBWsToCDTnPlot.R
fromGeneListToTSSbed.R		fromGeneListToTSSbed.R
makeBigHeatmap.R		makeBigHeatmap.R
makeBigHeatmapFromGeneList.R		makeBigHeatmapFromGeneList.R
makeCorrelationPlotAllSamples.R		makeCorrelationPlotAllSamples.R
makeHeatmap.R		makeHeatmap.R
makeKMplotsForProbeLists.R		makeKMplotsForProbeLists.R
makeMAplot.R		makeMAplot.R
previousrunGOforDEG.R		previousrunGOforDEG.R
processMOLNG.pl		processMOLNG.pl
reorderCDTbyDEG.R		reorderCDTbyDEG.R
runEdgeRdiffPeaks.R		runEdgeRdiffPeaks.R
runEdgeRgeneORpeak.R		runEdgeRgeneORpeak.R
runEdgeRrnaSeq.R		runEdgeRrnaSeq.R
runGOforDEG.R		runGOforDEG.R
split4CwithTable.pl		split4CwithTable.pl
wigToBigWig		wigToBigWig