MANIFEST.in
README.md
setup.cfg
setup.py
data/mini_nla_test.bam
data/mini_nla_test.bam.bai
data/mini_test.bed
singlecellmultiomics/__init__.py
singlecellmultiomics/version.py
singlecellmultiomics.egg-info/PKG-INFO
singlecellmultiomics.egg-info/SOURCES.txt
singlecellmultiomics.egg-info/dependency_links.txt
singlecellmultiomics.egg-info/requires.txt
singlecellmultiomics.egg-info/top_level.txt
singlecellmultiomics/alleleTools/__init__.py
singlecellmultiomics/alleleTools/alleleTools.py
singlecellmultiomics/bamProcessing/__init__.py
singlecellmultiomics/bamProcessing/alignment_view.py
singlecellmultiomics/bamProcessing/bamDuprate.py
singlecellmultiomics/bamProcessing/bamFeatureDensityVisualisation.py
singlecellmultiomics/bamProcessing/bamFilter.py
singlecellmultiomics/bamProcessing/bamFunctions.py
singlecellmultiomics/bamProcessing/bamPlateVisualisation.py
singlecellmultiomics/bamProcessing/bamPlotRTstats.py
singlecellmultiomics/bamProcessing/bamTabulator.py
singlecellmultiomics/bamProcessing/bamToCountTable.py
singlecellmultiomics/barcodeFileParser/__init__.py
singlecellmultiomics/barcodeFileParser/barcodeFileParser.py
singlecellmultiomics/countTableProcessing/__init__.py
singlecellmultiomics/countTableProcessing/downsampleDataFrame.py
singlecellmultiomics/fastqProcessing/__init__.py
singlecellmultiomics/fastqProcessing/fastqHandle.py
singlecellmultiomics/fastqProcessing/fastqIterator.py
singlecellmultiomics/features/__init__.py
singlecellmultiomics/features/features.py
singlecellmultiomics/fragment/__init__.py
singlecellmultiomics/fragment/fragment.py
singlecellmultiomics/fragment/nlaIII.py
singlecellmultiomics/libraryDetection/__init__.py
singlecellmultiomics/libraryDetection/sequencingLibraryListing.py
singlecellmultiomics/libraryProcessing/__init__.py
singlecellmultiomics/libraryProcessing/libraryStatistics.py
singlecellmultiomics/modularDemultiplexer/__init__.py
singlecellmultiomics/modularDemultiplexer/baseDemultiplexMethods.py
singlecellmultiomics/modularDemultiplexer/demultiplexedFastqConversion.py
singlecellmultiomics/modularDemultiplexer/demultiplexingStrategyLoader.py
singlecellmultiomics/modularDemultiplexer/demux.py
singlecellmultiomics/modularDemultiplexer/barcodes/celseq1.bc
singlecellmultiomics/modularDemultiplexer/barcodes/celseq2.bc
singlecellmultiomics/modularDemultiplexer/barcodes/celseq2_noNla.bc
singlecellmultiomics/modularDemultiplexer/barcodes/illumina_RP_indices.bc
singlecellmultiomics/modularDemultiplexer/barcodes/lennart96NLA.bc
singlecellmultiomics/modularDemultiplexer/barcodes/lk_virus1.bc
singlecellmultiomics/modularDemultiplexer/barcodes/maya_384NLA.bc
singlecellmultiomics/modularDemultiplexer/barcodes/maya_mspj1.bc
singlecellmultiomics/modularDemultiplexer/barcodes/nla_bisulfite.bc
singlecellmultiomics/modularDemultiplexer/barcodes/scartrace.bc
singlecellmultiomics/modularDemultiplexer/barcodes/scartraceBarcodes.bc
singlecellmultiomics/modularDemultiplexer/demultiplexModules/BULK_ILLUMINA.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/CELSeq1.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/CELSeq2.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/Hexamer.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/MSPJI.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/NLAIII.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/__init__.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/restrictionbisulfite.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/scCHIC.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/scartrace.py
singlecellmultiomics/modularDemultiplexer/indices/illumina_RP_indices.bc
singlecellmultiomics/modularDemultiplexer/indices/illumina_ThruPlex48S_indices.bc
singlecellmultiomics/modularDemultiplexer/indices/illumina_TruSeq_indices.bc
singlecellmultiomics/modularDemultiplexer/indices/illumina_i7_indices.bc
singlecellmultiomics/modularDemultiplexer/indices/illumina_merged_ThruPlex48S_RP.bc
singlecellmultiomics/modularDemultiplexer/indices/illumina_merged_iPCR_RP.bc
singlecellmultiomics/molecule/__init__.py
singlecellmultiomics/molecule/molecule.py
singlecellmultiomics/pyutils/__init__.py
singlecellmultiomics/pyutils/handlelimiter.py
singlecellmultiomics/pyutils/pyutils.py
singlecellmultiomics/statistic/__init__.py
singlecellmultiomics/statistic/allele.py
singlecellmultiomics/statistic/datatype.py
singlecellmultiomics/statistic/fragmentsize.py
singlecellmultiomics/statistic/mappingquality.py
singlecellmultiomics/statistic/methylation.py
singlecellmultiomics/statistic/oversequencing.py
singlecellmultiomics/statistic/plate.py
singlecellmultiomics/statistic/readcount.py
singlecellmultiomics/statistic/rejectionreasons.py
singlecellmultiomics/statistic/scchicligation.py
singlecellmultiomics/statistic/statistic.py
singlecellmultiomics/statistic/tag.py
singlecellmultiomics/statistic/trimming.py
singlecellmultiomics/tagtools/__init__.py
singlecellmultiomics/tagtools/tagtools.py
singlecellmultiomics/universalBamTagger/__init__.py
singlecellmultiomics/universalBamTagger/digest.py
singlecellmultiomics/universalBamTagger/mspjI.py
singlecellmultiomics/universalBamTagger/nlaIII.py
singlecellmultiomics/universalBamTagger/rna.py
singlecellmultiomics/universalBamTagger/scar.py
singlecellmultiomics/universalBamTagger/scchic.py
singlecellmultiomics/universalBamTagger/tag.py
singlecellmultiomics/universalBamTagger/taps.py
singlecellmultiomics/universalBamTagger/universalBamTagger.py
singlecellmultiomics/utils/__init__.py
singlecellmultiomics/utils/sequtils.py
singlecellmultiomics/utils/submission.py
singlecellmultiomics/variantCalling/variantExtraction.py