setup.py
MANIFEST.txt
LICENCE.txt
README.txt
pyCRAC/tests/test.novo
pyCRAC/tests/test.sh
pyCRAC/tests/test_coordinates.txt
pyCRAC/tests/test.gtf
pyCRAC/tests/test_f.fastq
pyCRAC/tests/test_f.fastq.gz
pyCRAC/tests/test_f_dm.fastq
pyCRAC/tests/test_r.fastq
pyCRAC/tests/test_r.fastq.gz
pyCRAC/tests/test_r_dm.fastq
pyCRAC/tests/indexes.txt
pyCRAC/tests/barcodes.txt
pyCRAC/tests/genes.lis
pyCRAC/Classes/NGSFormatWriters.py
pyCRAC/Classes/NGSFormatReaders.py
pyCRAC/Classes/PairedReads.py
pyCRAC/Classes/Pileups.py
pyCRAC/Classes/Aligner.py
pyCRAC/Classes/Motifs.py
pyCRAC/Classes/Barcodes.py
pyCRAC/Classes/Coverage.py
pyCRAC/Classes/Exceptions.py
pyCRAC/Classes/FDR.py
pyCRAC/Classes/Clustering
pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa
pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PE.py
pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PeakFinder.py
pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_SE.py
pyCRAC/kinetic_crac_pipeline/TrimNucs.py
pyCRAC/scripts/pybed2GTF.py
pyCRAC/scripts/pyGTF2bed.py
pyCRaC/scripts/pyGTF2bedGraph.py
pyCRAC/scripts/pyGTF2sgr.py
pyCRAC/scripts/pyNormalizeIntervalLengths.py
pyCRAC/scripts/pyFastqDuplicateRemover.py
pyCRAC/scripts/pyFastqJoiner.py
pyCRAC/scripts/pyFastqSplitter.py
pyCRAC/scripts/pyGetGeneNamesFromGTF.py
pyCRAC/scripts/pySelectMotifsFromGTF.py
pyCRAC/scripts/pyGetGTFSources.py
pyCRAC/scripts/pyFilterGTF.py
pyCRAC/scripts/pyFasta2tab.py
pyCRAC/scripts/pyAlignment2Tab.py
pyCRAC/scripts/pyExtractLinesFromGTF.py
pyCRAC/scripts/pyCheckGTFfile.py
pyCRAC/scripts/pyCalculateChromosomeLengths.py
pyCRAC/pyClusterReads.py
pyCRAC/pyCalculateFDRs.py
pyCRAC/pyCalculateMutationFrequencies.py
pyCRAC/pyBinCollector.py
pyCRAC/pyMotif.py
pyCRAC/pyPileup.py
pyCRAC/pyReadAligner.py
pyCRAC/pyReadCounters.py
pyCRAC/pyBarcodeFilter.py
pyCRAC/Parsers/Blast.py
pyCRAC/Parsers/GTF2.py
pyCRAC/Parsers/Novoalign.py
pyCRAC/Parsers/ParseAlignments.py
pyCRAC/Parsers/SAM.py
pyCRAC/Parsers/fasta2dict.py
pyCRAC/Parsers/tab2dict.py