README.md
The_pyCRAC_Manual.pdf
setup.py
pyCRAC/__init__.py
pyCRAC/pyBarcodeFilter.py
pyCRAC/pyBinCollector.py
pyCRAC/pyCalculateFDRs.py
pyCRAC/pyCalculateMutationFrequencies.py
pyCRAC/pyClusterReads.py
pyCRAC/pyMotif.py
pyCRAC/pyPileup.py
pyCRAC/pyReadAligner.py
pyCRAC/pyReadCounters.py
pyCRAC.egg-info/PKG-INFO
pyCRAC.egg-info/SOURCES.txt
pyCRAC.egg-info/dependency_links.txt
pyCRAC.egg-info/requires.txt
pyCRAC.egg-info/top_level.txt
pyCRAC/Classes/Aligner.py
pyCRAC/Classes/Barcodes.py
pyCRAC/Classes/Clustering.py
pyCRAC/Classes/Counters.py
pyCRAC/Classes/CountsNormalization.py
pyCRAC/Classes/Coverage.py
pyCRAC/Classes/Exceptions.py
pyCRAC/Classes/FDR.py
pyCRAC/Classes/Motifs.py
pyCRAC/Classes/NGSFormatReaders.py
pyCRAC/Classes/NGSFormatWriters.py
pyCRAC/Classes/PairedReads.py
pyCRAC/Classes/Pileups.py
pyCRAC/Classes/__init__.py
pyCRAC/Methods/__init__.py
pyCRAC/Parsers/GTF2.py
pyCRAC/Parsers/Novoalign.py
pyCRAC/Parsers/ParseAlignments.py
pyCRAC/Parsers/SAM.py
pyCRAC/Parsers/__init__.py
pyCRAC/Parsers/fasta2dict.py
pyCRAC/Parsers/tab2dict.py
pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa
pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab
pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt
pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf
pyCRAC/scripts/pyAlignment2Tab.py
pyCRAC/scripts/pyCalculateChromosomeLengths.py
pyCRAC/scripts/pyCheckGTFfile.py
pyCRAC/scripts/pyExtractLinesFromGTF.py
pyCRAC/scripts/pyFasta2tab.py
pyCRAC/scripts/pyFastqDuplicateRemover.py
pyCRAC/scripts/pyFastqJoiner.py
pyCRAC/scripts/pyFastqSplitter.py
pyCRAC/scripts/pyFilterGTF.py
pyCRAC/scripts/pyGTF2bed.py
pyCRAC/scripts/pyGTF2bedGraph.py
pyCRAC/scripts/pyGTF2sgr.py
pyCRAC/scripts/pyGetGTFSources.py
pyCRAC/scripts/pyGetGeneNamesFromGTF.py
pyCRAC/scripts/pyNormalizeIntervalLengths.py
pyCRAC/scripts/pySelectMotifsFromGTF.py
pyCRAC/scripts/pybed2GTF.py
tests/barcodes.txt
tests/genes.list
tests/indexes.txt
tests/test.gtf
tests/test.novo
tests/test.sh
tests/test_coordinates.txt
tests/test_f.fastq
tests/test_f.fastq.gz
tests/test_f_dm.fastq
tests/test_r.fastq
tests/test_r.fastq.gz
tests/test_r_dm.fastq