GitHub - williampei1610/NGS: Scripts for next generation sequencing

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Scripts for next generation sequencing

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Name		Name	Last commit message	Last commit date
Latest commit History 265 Commits
AS		AS
test_dir		test_dir
trash		trash
.overlappedRegionsAmongMultipleSamples.py.swp		.overlappedRegionsAmongMultipleSamples.py.swp
1.py		1.py
1.sh		1.sh
16S.sh		16S.sh
AtannoByLocus.py		AtannoByLocus.py
CreateSnpTreeSeq.py		CreateSnpTreeSeq.py
DESeq2.indev.sh		DESeq2.indev.sh
DESeq2.ori.sh		DESeq2.ori.sh
DESeq2.sh		DESeq2.sh
DEXSeq.sh		DEXSeq.sh
DE_analysis.pl		DE_analysis.pl
DE_genes.summary.py		DE_genes.summary.py
DE_methylated_gene.summary.chenwei.py		DE_methylated_gene.summary.chenwei.py
DMR.sh		DMR.sh
DMR2.sh		DMR2.sh
Fst_estimate.ct.r		Fst_estimate.ct.r
GEO_upload.sh		GEO_upload.sh
I_TASSER.sh		I_TASSER.sh
I_TASSER_bat.py		I_TASSER_bat.py
ListFileSummaryDoc.py		ListFileSummaryDoc.py
MethylExtractBSCR.pl		MethylExtractBSCR.pl
P450_clan_family_anno.py		P450_clan_family_anno.py
PI_ratio.py		PI_ratio.py
Peak.summary.py		Peak.summary.py
RPKM_saturationSummary.py		RPKM_saturationSummary.py
SSRidentificationPrimerDesignEpcrSummarizeAmplicon.py		SSRidentificationPrimerDesignEpcrSummarizeAmplicon.py
STAR_geneCnt_integrate.py		STAR_geneCnt_integrate.py
STAR_read_mapSummary.py		STAR_read_mapSummary.py
SingleC_MetLevel.pl		SingleC_MetLevel.pl
TCGA_UUID.py		TCGA_UUID.py
Trinotate.build.sh		Trinotate.build.sh
Unmapped_summary.py		Unmapped_summary.py
WGCNA.r		WGCNA.r
WGCNA.sh		WGCNA.sh
a.markdown.r		a.markdown.r
addExtraColumn.py		addExtraColumn.py
addUser.sh		addUser.sh
affy_deGenes.sh		affy_deGenes.sh
affy_full.sh		affy_full.sh
afterBlastParse.py		afterBlastParse.py
afterRunGOseq.py		afterRunGOseq.py
afterRunGOseqGeneral.py		afterRunGOseqGeneral.py
afterRunclusterProfileGO.py		afterRunclusterProfileGO.py
afterRunclusterProfileKEGG.py		afterRunclusterProfileKEGG.py
afterRunclusterProfileSelf.py		afterRunclusterProfileSelf.py
afteredgeRanalyze_diffexpr.py		afteredgeRanalyze_diffexpr.py
airflowDagGen.py		airflowDagGen.py
alignIsoformers.py		alignIsoformers.py
alphabetCnt.py		alphabetCnt.py
analyzeFimo.py		analyzeFimo.py
animalMiRNATargetPredict.py		animalMiRNATargetPredict.py
animalMiRNATargetPredict2.py		animalMiRNATargetPredict2.py
animalMiRNATargetSite.py		animalMiRNATargetSite.py
annoGroupUseEnsembl.py		annoGroupUseEnsembl.py
annoscriptConfig.sh		annoscriptConfig.sh
annotateTranscript.py		annotateTranscript.py
annotate_gene_cluster.py		annotate_gene_cluster.py
anova.sh		anova.sh
anovaTwoFactor.sh		anovaTwoFactor.sh
aracyc.py		aracyc.py
asType.py		asType.py
ascp.py		ascp.py
batchTcoffee.py		batchTcoffee.py
bdgToWig.py		bdgToWig.py
bed12ToCircAnno.py		bed12ToCircAnno.py
bed12Tobed6.py		bed12Tobed6.py
bedCovrageUseWig.py		bedCovrageUseWig.py
bedCovrageUseWig.readBedIn.py		bedCovrageUseWig.readBedIn.py
bedToWig.py		bedToWig.py
bedgraphToWig.py		bedgraphToWig.py
bedpe_pos_len.Summay.bak.py		bedpe_pos_len.Summay.bak.py
bedpe_pos_len.Summay.py		bedpe_pos_len.Summay.py
bedpe_pos_len.py		bedpe_pos_len.py
bedpe_pos_len.stat.py		bedpe_pos_len.stat.py
bedtools_coverage.Summary.py		bedtools_coverage.Summary.py
bedtools_genomecov.Summary.py		bedtools_genomecov.Summary.py
bedtools_genomecov.py		bedtools_genomecov.py
bfkmp.py		bfkmp.py
biclusterDraw.py		biclusterDraw.py
biclusterExtractGeneClass.py		biclusterExtractGeneClass.py
binCnt_summary.py		binCnt_summary.py
binRegionForCovRpkm.py		binRegionForCovRpkm.py
binRegions.py		binRegions.py
binRegions2.py		binRegions2.py
binTranscriptome.py		binTranscriptome.py
binmRNARegions.py		binmRNARegions.py
biogrid.extract.py		biogrid.extract.py
biomartXML.py		biomartXML.py
bismark_filterC_count.Summary.py		bismark_filterC_count.Summary.py
bismark_methylation_extractor_split.py		bismark_methylation_extractor_split.py
bismark_methylation_extractor_split_toWig.py		bismark_methylation_extractor_split_toWig.py
bismark_saturation.Summary.py		bismark_saturation.Summary.py
bismark_saturation.py		bismark_saturation.py
bisulfite_conversion_rate.py		bisulfite_conversion_rate.py
bisulfite_conversion_rateSummary.py		bisulfite_conversion_rateSummary.py
blast.py		blast.py
blastParse.old.py		blastParse.old.py