Name		Name	Last commit message	Last commit date
Latest commit History 1 Commits
2script.R		2script.R
3script.R		3script.R
4StateAnalysis.R		4StateAnalysis.R
ALLintro.R		ALLintro.R
ASCII.R		ASCII.R
AT-GC.sh		AT-GC.sh
Analysis_StateModel.R		Analysis_StateModel.R
BaumWelchNB.R		BaumWelchNB.R
BernsteinInput_HMMDiscretizeCHIP.R		BernsteinInput_HMMDiscretizeCHIP.R
BinChromHMM2Bed.py		BinChromHMM2Bed.py
Config.py		Config.py
CurrentMkChangeNotes.py		CurrentMkChangeNotes.py
DiagnosisH1hESCInfection.R		DiagnosisH1hESCInfection.R
DiagnosisViralInfection.R		DiagnosisViralInfection.R
EMalgorithms.R		EMalgorithms.R
Exception.R		Exception.R
Fasq-H1parser.py		Fasq-H1parser.py
FasqH1md5parser.py		FasqH1md5parser.py
FastQValidatorTest.sh		FastQValidatorTest.sh
FileDownloader.py		FileDownloader.py
GEOquery.R		GEOquery.R
GO-compute-hyper-pvals.R		GO-compute-hyper-pvals.R
GO_ALL.R		GO_ALL.R
GO_analysis.R		GO_analysis.R
GbIndex.py		GbIndex.py
Gem-Fastq-2-Sam.sh		Gem-Fastq-2-Sam.sh
Gem1.366-Fastq-2-Sam.sh		Gem1.366-Fastq-2-Sam.sh
GenomePartition.py		GenomePartition.py
GenomeSeqs.py		GenomeSeqs.py
GenomicFeatures.R		GenomicFeatures.R
GenomicRangesIntroduction.R		GenomicRangesIntroduction.R
GenomicRangesUseCases.R		GenomicRangesUseCases.R
Gviz.R		Gviz.R
H1BamToBed.sh		H1BamToBed.sh
H1BigTableALLPipeline.sh		H1BigTableALLPipeline.sh
H1BigTableALLonlyID.sh		H1BigTableALLonlyID.sh
H1BigTableDiscretizedPipeline.sh		H1BigTableDiscretizedPipeline.sh
H1BigTablePipeline.sh		H1BigTablePipeline.sh
H1BigTablePipeline_onlyID.sh		H1BigTablePipeline_onlyID.sh
H1Binit3000pipeline.sh		H1Binit3000pipeline.sh
H1Binit300Pipeline.sh		H1Binit300Pipeline.sh
H1BinitLiftedFilePipeline.sh		H1BinitLiftedFilePipeline.sh
H1BinitLiftedFilePipeline3000bp.sh		H1BinitLiftedFilePipeline3000bp.sh
H1CheckLiftOver.sh		H1CheckLiftOver.sh
H1LiftOverPipeline.sh		H1LiftOverPipeline.sh
H1Rebinit300Pipeline.sh		H1Rebinit300Pipeline.sh
H1Rename.py		H1Rename.py
H1RenameNone.py		H1RenameNone.py
H1_chromHMMatin.R		H1_chromHMMatin.R
H1md5parser.py		H1md5parser.py
H1parser.py		H1parser.py
HMMDiscretizeCHIP.R		HMMDiscretizeCHIP.R
HMMDiscretizeCHIP_list.R		HMMDiscretizeCHIP_list.R
InfoExtractors.py		InfoExtractors.py
Integration-NP.R		Integration-NP.R
KG2.sh		KG2.sh
KG3.sh		KG3.sh
KGRef2.sh		KGRef2.sh
KGRef3.sh		KGRef3.sh
KGcgap.sh		KGcgap.sh
KGpath.sh		KGpath.sh
KGpathArchaea.sh		KGpathArchaea.sh
KGprocess.sh		KGprocess.sh
MMgemUniqueMap.sh		MMgemUniqueMap.sh
NoteStore.py		NoteStore.py
Old_NewGem.R		Old_NewGem.R
OverlapEncodings.R		OverlapEncodings.R
PCACheck.R		PCACheck.R
PCA_3000plots.R		PCA_3000plots.R
PCA_300plots.R		PCA_300plots.R
PCA_4states.R		PCA_4states.R
Pipeline.py		Pipeline.py
PostProcessor.py		PostProcessor.py
RCytoscape.R		RCytoscape.R
README.md		README.md
RNAseqAnalysis.R		RNAseqAnalysis.R
RamiGO.R		RamiGO.R
RandomForestClassifier.R		RandomForestClassifier.R
ReMapFastqPipeline.sh		ReMapFastqPipeline.sh
ReMapFastqPipelineGem1.366.sh		ReMapFastqPipelineGem1.366.sh
ReMapFastqPipelineGem1.366_qualityIGNORE.sh		ReMapFastqPipelineGem1.366_qualityIGNORE.sh
ReMapFastqUnmaskedPipeline.sh		ReMapFastqUnmaskedPipeline.sh
Rename_pfFilename.sh		Rename_pfFilename.sh
RnwToMd.R		RnwToMd.R
RunTest.sh		RunTest.sh
SubstringDict.py		SubstringDict.py
SuffixTree.py		SuffixTree.py
SweaveCache.R		SweaveCache.R
TBase.py		TBase.py
TBinaryProtocol.py		TBinaryProtocol.py
TCompactProtocol.py		TCompactProtocol.py
THttpClient.py		THttpClient.py
THttpServer.py		THttpServer.py
TNonblockingServer.py		TNonblockingServer.py
TProcessPoolServer.py		TProcessPoolServer.py
TProtocol.py		TProtocol.py
TSCons.py		TSCons.py
TSSLSocket.py		TSSLSocket.py
TSS_H1.R		TSS_H1.R
TSerialization.py		TSerialization.py

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