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README.md
README.md
 
 
addEffectiveNumberToSummaryFiles.R
addEffectiveNumberToSummaryFiles.R
 
 
analyzeCollapsedFastq.py
analyzeCollapsedFastq.py
 
 
checkPrecursorStructInPrimaryStruct.R
checkPrecursorStructInPrimaryStruct.R
 
 
checkSNPLocation.R
checkSNPLocation.R
 
 
collapseFastqFiles.py
collapseFastqFiles.py
 
 
downloadCGCFiles.py
downloadCGCFiles.py
 
 
downloadTCGAFiles.py
downloadTCGAFiles.py
 
 
editManifestFile.R
editManifestFile.R
 
 
editTertiaryStructure.py
editTertiaryStructure.py
 
 
formatManifestFile.R
formatManifestFile.R
 
 
formatmiRBaseData.R
formatmiRBaseData.R
 
 
get-all-tumor-fidelity.R
get-all-tumor-fidelity.R
 
 
get-miRNA-coordinates.py
get-miRNA-coordinates.py
 
 
get-new-motifs.py
get-new-motifs.py
 
 
get5P3PRatio.R
get5P3PRatio.R
 
 
get5PFidelityByMirna.R
get5PFidelityByMirna.R
 
 
get5PMotifs.R
get5PMotifs.R
 
 
getAverageTissueFidelity.R
getAverageTissueFidelity.R
 
 
getCommonMotifReadsFromCollapsedFastq.py
getCommonMotifReadsFromCollapsedFastq.py
 
 
getConsensusPath.R
getConsensusPath.R
 
 
getConservedExtendedSecondaryStructure.R
getConservedExtendedSecondaryStructure.R
 
 
getEffectiveByTissue.R
getEffectiveByTissue.R
 
 
getEffectiveNumber.R
getEffectiveNumber.R
 
 
getExtendedSequenceFasta.R
getExtendedSequenceFasta.R
 
 
getFidelity5PByGeneExpression.R
getFidelity5PByGeneExpression.R
 
 
getFidelityByGene.R
getFidelityByGene.R
 
 
getHighestExpressedIsomir.R
getHighestExpressedIsomir.R
 
 
getIncreasingSecondaryStructure.py
getIncreasingSecondaryStructure.py
 
 
getLongestRNAStem.R
getLongestRNAStem.R
 
 
getMORBasePairRatio.R
getMORBasePairRatio.R
 
 
getMatureSequenceContext.R
getMatureSequenceContext.R
 
 
getMoRStructsSameBrackets.R
getMoRStructsSameBrackets.R
 
 
getMotifCoverage.R
getMotifCoverage.R
 
 
getMotifsPositions.R
getMotifsPositions.R
 
 
getPatientFidelityRPMByTumor.R
getPatientFidelityRPMByTumor.R
 
 
getSequenceReads.R
getSequenceReads.R
 
 
getTumorManifest.R
getTumorManifest.R
 
 
getUniqueMirbaseMotif.R
getUniqueMirbaseMotif.R
 
 
getUniqueMotif.py
getUniqueMotif.py
 
 
getUniqueMotifs.R
getUniqueMotifs.R
 
 
locateIUPACMotif.R
locateIUPACMotif.R
 
 
mapTemplatedBases.R
mapTemplatedBases.R
 
 
miRNA-fidelity-5p-summary-files.R
miRNA-fidelity-5p-summary-files.R
 
 
miRNA-start-freq-by-level.R
miRNA-start-freq-by-level.R
 
 
normalization-FKQM-UQ-files.R
normalization-FKQM-UQ-files.R
 
 
normalization-miRNA-files.R
normalization-miRNA-files.R
 
 
passengerStrandPredictionAnalysis.R
passengerStrandPredictionAnalysis.R
 
 
readsByTumor.R
readsByTumor.R
 
 
summarizeCollapsedFastq.py
summarizeCollapsedFastq.py
 
 

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