Name
..
.ipynb_checkpoints
ExtractFromTCGA
TestPipeline
CheckFASTA.ipynb
CheckVCF.ipynb
Compare_TCGA_RNAseq_WXS.ipynb
Compare_TCGA_RNAseq_WXS_Germline_AllFiles.ipynb
Compare_TCGA_RNAseq_WXS_Germline_OneFile.ipynb
Compare_TCGA_RNAseq_WXS_IDH1_only.ipynb
Compare_TCGA_RNAseq_WXS_allOverlapSites.ipynb
FindStudiesWithBrafV600Mutated.ipynb
GenerateEmptyPicklesForEachSpecies.ipynb
MaskingGenomeWithSnp_Specie.ipynb
MaskingGenomeWithSnp_human.ipynb
MergeViralAndBacterial.ipynb
ParseAndMergeBamReadCount.ipynb
Pull_TCGA_meta_data.ipynb
README_TCGA_benchmark.ipynb
Scratch.ipynb
UCSCBedsToSpecieBeds.ipynb
Untitled.ipynb
Untitled1.ipynb
Untitled2.ipynb
Untitled3.ipynb
Untitled4.ipynb
basicQualityCheck.ipynb
checkAllelicSpecificExpression.ipynb
checkLiftByChromOverCoverage.ipynb
checkSNPsMouse.ipynb
conver_bed_to_uscs.ipynb
correlateSites__MyPipe_and_TcgaPipe.ipynb
downloadingVCFs.ipynb
evaluateDuplicateRemovalAllelicFraction.ipynb
evaluateDuplicateRemovalAllelicReadCounts.ipynb
findOutWhereTheSiteAreFrom.ipynb
identify_TCGA_WXS_RNAseq_runs.ipynb
liftOverAllSNPCorrdinates.ipynb
mergeBamReadCount.v2.ipynb
mergeMicrobeFastas.ipynb
mergeTCGA_VCF.ipynb
old_BuildReferenceWithMicrobes.ipynb
old_MaskingGenomeWithSnp_Specie.ipynb
old_ParseAndMergeBamReadCount.v2.ipynb
old_downloadTCGA_LGG.ipynb
parquet.ipynb
pyLiftOver.ipynb
remergeBasedOnSRR_RunIDs.ipynb
scratch_delete.ipynb
testOne.ipynb
uploadDataToSynapseList.ipynb
uploadMetaDataToSynapseList.ipynb
single_snp.py