GitHub - spundhir/RNA-Seq: My Scripts for the analysis of RNA-seq data

# RNA-Seq

Name		Name	Last commit message	Last commit date
archieve		archieve
flagCluster		flagCluster
old		old
source		source
._SNAP-CUTANA_K-MetStat_Panel_ShellScript.sh		._SNAP-CUTANA_K-MetStat_Panel_ShellScript.sh
._estimate-insert-sizes		._estimate-insert-sizes
ADAPTER_ILLUMINA		ADAPTER_ILLUMINA
ADAPTER_ILLUMINA.pdf		ADAPTER_ILLUMINA.pdf
BARCODES_CUTANA		BARCODES_CUTANA
README.rst		README.rst
bam2mirdeep2.pl		bam2mirdeep2.pl
bed2intersect.pl		bed2intersect.pl
bed2seq.pl		bed2seq.pl
bed2uniq.pl		bed2uniq.pl
checkRNASeqFormat.pl		checkRNASeqFormat.pl
clipAdapter.pl		clipAdapter.pl
colorUCSCTrack.pl		colorUCSCTrack.pl
computeDESeqMatrix.pl		computeDESeqMatrix.pl
convertId.R		convertId.R
coor2bginfo.pl		coor2bginfo.pl
coor2fasta		coor2fasta
coor2intersect.pl		coor2intersect.pl
coor2maf.pl		coor2maf.pl
coor2overlap.pl		coor2overlap.pl
coor2seq.pl		coor2seq.pl
coor2wig.pl		coor2wig.pl
createBedGraph.pl		createBedGraph.pl
cuffAnalysis		cuffAnalysis
cutana.sh		cutana.sh
deseq.R		deseq.R
deseq2.R		deseq2.R
dexseq.R		dexseq.R
edger.R		edger.R
editMaf.pl		editMaf.pl
editMafNew.pl		editMafNew.pl
estimateInsertSize		estimateInsertSize
estimateInsertSize.sh		estimateInsertSize.sh
fasta2clustal.pl		fasta2clustal.pl
filterDBAoutput.pl		filterDBAoutput.pl
fq_all2std.pl		fq_all2std.pl
gene2ptbp1		gene2ptbp1
gtf2expr		gtf2expr
gtf2expr.R		gtf2expr.R
gtf2fasta.sh		gtf2fasta.sh
indexBG.pl		indexBG.pl
indexMap.sh		indexMap.sh
kallisto2matrix.R		kallisto2matrix.R
maf-join.py		maf-join.py
mapPEReads.sh		mapPEReads.sh
mapSEReads.sh		mapSEReads.sh
mapStat.sh		mapStat.sh
matrix2clustering.R		matrix2clustering.R
matrix2heatmap.R		matrix2heatmap.R
mirbase2bed.pl		mirbase2bed.pl
parseNewick.pl		parseNewick.pl
parse_spliceR.R		parse_spliceR.R
plotBlockStat.r		plotBlockStat.r
plotReadProfile.x		plotReadProfile.x
plotblockProfile.r		plotblockProfile.r
ptc_analysis.R		ptc_analysis.R
pvclust2bed.pl		pvclust2bed.pl
pwm2seqlogo.R		pwm2seqlogo.R
qualStat		qualStat
qualityCheck.sh		qualityCheck.sh
readPosBias.R		readPosBias.R
rnaSeqAna.sh		rnaSeqAna.sh
rnaSeqAnaBed.sh		rnaSeqAnaBed.sh
rnaSeqAnaSperm.sh		rnaSeqAnaSperm.sh
rnapipe2heatmap		rnapipe2heatmap
runfoldalign.sh		runfoldalign.sh
sam2bam		sam2bam
sam2bedGraph		sam2bedGraph
screenShotUCSC.R		screenShotUCSC.R
seqIdentity.pl		seqIdentity.pl
shuffle		shuffle
splicing2win		splicing2win
splicing2win1		splicing2win1
splicing2win2		splicing2win2
splicingAna		splicingAna
sra2fastq.sh		sra2fastq.sh
subSampleBAM.pl		subSampleBAM.pl
subSampleFasta.sh		subSampleFasta.sh
submitJob.pl		submitJob.pl
submitJob.sh		submitJob.sh
track2pdf.pl		track2pdf.pl
trimAdapters.sh		trimAdapters.sh
txt2html.pl		txt2html.pl
ucsc2pdf		ucsc2pdf
uniqLongestGene.pl		uniqLongestGene.pl
validateDiffProcessing.pl		validateDiffProcessing.pl

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