LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
data/chic_test_region.bam
data/chic_test_region.bam.bai
data/mini_nla_test.bam
data/mini_nla_test.bam.bai
data/mini_test.bed
data/ref.fa
data/ref.fa.fai
docs/conf.py
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/FACS/__init__.py
singlecellmultiomics/FACS/facs.py
singlecellmultiomics/FACS/trajectory.py
singlecellmultiomics/alleleTools/__init__.py
singlecellmultiomics/alleleTools/alleleTools.py
singlecellmultiomics/alleleTools/heterozygousSNPedit.py
singlecellmultiomics/bamProcessing/__init__.py
singlecellmultiomics/bamProcessing/alignment_view.py
singlecellmultiomics/bamProcessing/bamAnalyzeCutDistances.py
singlecellmultiomics/bamProcessing/bamBinCounts.py
singlecellmultiomics/bamProcessing/bamCompare.py
singlecellmultiomics/bamProcessing/bamCopyNumber.py
singlecellmultiomics/bamProcessing/bamCountRegions.py
singlecellmultiomics/bamProcessing/bamDinucleotideDistribution.py
singlecellmultiomics/bamProcessing/bamDuprate.py
singlecellmultiomics/bamProcessing/bamExtractNearMolecules.py
singlecellmultiomics/bamProcessing/bamExtractRandomPrimerStats.py
singlecellmultiomics/bamProcessing/bamExtractSamples.py
singlecellmultiomics/bamProcessing/bamExtractVariants.py
singlecellmultiomics/bamProcessing/bamFeatureDensityVisualisation.py
singlecellmultiomics/bamProcessing/bamFeatures.py
singlecellmultiomics/bamProcessing/bamFilter.py
singlecellmultiomics/bamProcessing/bamFunctions.py
singlecellmultiomics/bamProcessing/bamMappingRate.py
singlecellmultiomics/bamProcessing/bamMatchGATKBQSRReport.py
singlecellmultiomics/bamProcessing/bamMethylationCutDistance.py
singlecellmultiomics/bamProcessing/bamMutProfiler.py
singlecellmultiomics/bamProcessing/bamOverseq.py
singlecellmultiomics/bamProcessing/bamPlateVisualisation.py
singlecellmultiomics/bamProcessing/bamPlotRTstats.py
singlecellmultiomics/bamProcessing/bamReadGroupFormat.py
singlecellmultiomics/bamProcessing/bamSetReadGroup.py
singlecellmultiomics/bamProcessing/bamSplitByTag.py
singlecellmultiomics/bamProcessing/bamTabulator.py
singlecellmultiomics/bamProcessing/bamToBigWig.py
singlecellmultiomics/bamProcessing/bamToCountTable.py
singlecellmultiomics/bamProcessing/bamToMethylationAndCopyNumber.py
singlecellmultiomics/bamProcessing/bamToMethylationCalls.py
singlecellmultiomics/bamProcessing/bamToNucleosomePositions.py
singlecellmultiomics/bamProcessing/bamToRNACounts.py
singlecellmultiomics/bamProcessing/estimateTapsConversionEfficiency.py
singlecellmultiomics/bamProcessing/pileup.py
singlecellmultiomics/bamProcessing/plotRegion.py
singlecellmultiomics/bamProcessing/scmoConvert.py
singlecellmultiomics/bamProcessing/soft_clip_filter.py
singlecellmultiomics/bamProcessing/split_bam_by_cluster.py
singlecellmultiomics/bamProcessing/split_double_BAM.py
singlecellmultiomics/bamProcessing/structureTensor.py
singlecellmultiomics/bamProcessing/variantStats.py
singlecellmultiomics/barcodeFileParser/__init__.py
singlecellmultiomics/barcodeFileParser/barcodeFileParser.py
singlecellmultiomics/countTableProcessing/__init__.py
singlecellmultiomics/countTableProcessing/correct_count_table_bias.py
singlecellmultiomics/countTableProcessing/downsampleDataFrame.py
singlecellmultiomics/fastaProcessing/__init__.py
singlecellmultiomics/fastaProcessing/createMappabilityIndex.py
singlecellmultiomics/fastaProcessing/fastaCreateDict.py
singlecellmultiomics/fastaProcessing/fastaHandle.py
singlecellmultiomics/fastaProcessing/fastaMaskVariants.py
singlecellmultiomics/fastqProcessing/__init__.py
singlecellmultiomics/fastqProcessing/fastqHandle.py
singlecellmultiomics/fastqProcessing/fastqIterator.py
singlecellmultiomics/fastqProcessing/fastq_filter_by_dt.py
singlecellmultiomics/fastqProcessing/trim_vasa.py
singlecellmultiomics/features/__init__.py
singlecellmultiomics/features/exonGTFtoIntronGTF.py
singlecellmultiomics/features/features.py
singlecellmultiomics/fragment/__init__.py
singlecellmultiomics/fragment/chic.py
singlecellmultiomics/fragment/fragment.py
singlecellmultiomics/fragment/nlaIII.py
singlecellmultiomics/fragment/scartrace.py
singlecellmultiomics/libraryDetection/__init__.py
singlecellmultiomics/libraryDetection/sequencingLibraryListing.py
singlecellmultiomics/libraryProcessing/__init__.py
singlecellmultiomics/libraryProcessing/libraryStatistics.py
singlecellmultiomics/libraryProcessing/sample_sheet.py
singlecellmultiomics/libraryProcessing/scsortchicfeaturedensitytable.py
singlecellmultiomics/libraryProcessing/scsortchicqc.py
singlecellmultiomics/libraryProcessing/scsortchicstats.py
singlecellmultiomics/methylation/__init__.py
singlecellmultiomics/methylation/bam_to_methylation_bw.py
singlecellmultiomics/methylation/methylation.py
singlecellmultiomics/methylation/methylationtab_to_bed.py
singlecellmultiomics/modularDemultiplexer/__init__.py
singlecellmultiomics/modularDemultiplexer/baseDemultiplexMethods.py
singlecellmultiomics/modularDemultiplexer/demultiplexedFastqConversion.py
singlecellmultiomics/modularDemultiplexer/demultiplexingStrategyLoader.py
singlecellmultiomics/modularDemultiplexer/demux.py
singlecellmultiomics/modularDemultiplexer/barcodes/10x_3M-february-2018.bc.gz
singlecellmultiomics/modularDemultiplexer/barcodes/CS2_scattered.bc
singlecellmultiomics/modularDemultiplexer/barcodes/CS2_scattered_8bp.bc
singlecellmultiomics/modularDemultiplexer/barcodes/DamID2.bc
singlecellmultiomics/modularDemultiplexer/barcodes/DamID2_384_CelSeq2.barcodes.tsv
singlecellmultiomics/modularDemultiplexer/barcodes/DamID2_8bp.bc
singlecellmultiomics/modularDemultiplexer/barcodes/DamID2_scattered.bc
singlecellmultiomics/modularDemultiplexer/barcodes/DamID2_scattered_8bp.bc
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/DamID.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/Hexamer.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/MSPJI.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/NLAIII.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/__init__.py
singlecellmultiomics/modularDemultiplexer/demultiplexModules/chromium_10x.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/chic.py
singlecellmultiomics/molecule/consensus.py
singlecellmultiomics/molecule/featureannotatedmolecule.py
singlecellmultiomics/molecule/filter.py
singlecellmultiomics/molecule/fourthiouridine.py
singlecellmultiomics/molecule/iterator.py
singlecellmultiomics/molecule/molecule.py
singlecellmultiomics/molecule/nlaIII.py
singlecellmultiomics/molecule/rna.py
singlecellmultiomics/molecule/scartrace.py
singlecellmultiomics/molecule/taps.py
singlecellmultiomics/molecule/consensus_model/nla_140bp_pe_juan_1M.pickle
singlecellmultiomics/molecule/consensus_model/sk_NR3_mf3_trained_hard_fit_9939.h5
singlecellmultiomics/pyutils/__init__.py
singlecellmultiomics/pyutils/handlelimiter.py
singlecellmultiomics/pyutils/pyutils.py
singlecellmultiomics/snakemake_workflows/scmo_workflow.py
singlecellmultiomics/snakemake_workflows/_general/sge_wrapper.py
singlecellmultiomics/snakemake_workflows/_general/slurm_wrapper.py
singlecellmultiomics/snakemake_workflows/call_sc_variants/Snakefile
singlecellmultiomics/snakemake_workflows/call_sc_variants/config.json
singlecellmultiomics/snakemake_workflows/call_variants/Snakefile
singlecellmultiomics/snakemake_workflows/call_variants/config.json
singlecellmultiomics/snakemake_workflows/chic/Snakefile
singlecellmultiomics/snakemake_workflows/chic/config.json
singlecellmultiomics/snakemake_workflows/chic_allelic/Snakefile
singlecellmultiomics/snakemake_workflows/chic_allelic/config.json
singlecellmultiomics/snakemake_workflows/chict/Snakefile
singlecellmultiomics/snakemake_workflows/chict/config.json
singlecellmultiomics/snakemake_workflows/cs2/Snakefile
singlecellmultiomics/snakemake_workflows/cs2/config.json
singlecellmultiomics/snakemake_workflows/cs2_scmo/Snakefile
singlecellmultiomics/snakemake_workflows/cs2_scmo/config.json
singlecellmultiomics/snakemake_workflows/demux/demux.smk
singlecellmultiomics/snakemake_workflows/merge_fastq/Snakefile
singlecellmultiomics/snakemake_workflows/mutect_bulk/Snakefile
singlecellmultiomics/snakemake_workflows/mutect_bulk/config.json
singlecellmultiomics/snakemake_workflows/nlaIII/README.MD
singlecellmultiomics/snakemake_workflows/nlaIII/Snakefile
singlecellmultiomics/snakemake_workflows/nlaIII/config.json
singlecellmultiomics/snakemake_workflows/scartrace/Snakefile
singlecellmultiomics/snakemake_workflows/scartrace/config.json
singlecellmultiomics/snakemake_workflows/vasa/Snakefile
singlecellmultiomics/snakemake_workflows/vasa/config.json
singlecellmultiomics/statistic/__init__.py
singlecellmultiomics/statistic/allele.py
singlecellmultiomics/statistic/cellreadcount.py
singlecellmultiomics/statistic/conversions.py
singlecellmultiomics/statistic/datatype.py
singlecellmultiomics/statistic/fragmentsize.py
singlecellmultiomics/statistic/lorenz.py
singlecellmultiomics/statistic/mappingquality.py
singlecellmultiomics/statistic/methylation.py
singlecellmultiomics/statistic/oversequencing.py
singlecellmultiomics/statistic/plate.py
singlecellmultiomics/statistic/plate2.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/tags/__init__.py
singlecellmultiomics/tags/tags.py
singlecellmultiomics/tags/write_tags_md.py
singlecellmultiomics/tagtools/__init__.py
singlecellmultiomics/tagtools/tagtools.py
singlecellmultiomics/universalBamTagger/4SUtagger.py
singlecellmultiomics/universalBamTagger/__init__.py
singlecellmultiomics/universalBamTagger/bamtagmultiome.py
singlecellmultiomics/universalBamTagger/bamtagmultiome_multi.py
singlecellmultiomics/universalBamTagger/customreads.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/tagging.py
singlecellmultiomics/universalBamTagger/taps.py
singlecellmultiomics/universalBamTagger/tapsTabulator.py
singlecellmultiomics/universalBamTagger/tapsTagger.py
singlecellmultiomics/universalBamTagger/universalBamTagger.py
singlecellmultiomics/utils/__init__.py
singlecellmultiomics/utils/base_call_covariates.py
singlecellmultiomics/utils/bdbbio.py
singlecellmultiomics/utils/bdbplot.py
singlecellmultiomics/utils/bdbsstats.py
singlecellmultiomics/utils/bigWigDiff.py
singlecellmultiomics/utils/binning.py
singlecellmultiomics/utils/blockzip.py
singlecellmultiomics/utils/copyNumberStatePlotter.py
singlecellmultiomics/utils/export.py
singlecellmultiomics/utils/ftp_upload.py
singlecellmultiomics/utils/html.py
singlecellmultiomics/utils/iteration.py
singlecellmultiomics/utils/lda.py
singlecellmultiomics/utils/organoidTools.py
singlecellmultiomics/utils/pandas.py
singlecellmultiomics/utils/path.py
singlecellmultiomics/utils/plotting.py
singlecellmultiomics/utils/poolutils.py
singlecellmultiomics/utils/prefetch.py
singlecellmultiomics/utils/sequtils.py
singlecellmultiomics/utils/stats.py
singlecellmultiomics/utils/submission.py
singlecellmultiomics/variants/__init__.py
singlecellmultiomics/variants/plotCovariates.py
singlecellmultiomics/variants/postProcessVariants.py
singlecellmultiomics/variants/substitutions.py
singlecellmultiomics/variants/variantWrapper.py
singlecellmultiomics/variants/vcfFilterAlleleFreq.py
singlecellmultiomics/variants/vcfMutProfiler.py
singlecellmultiomics/variants/vcf_utils.py
tests/_write_debug.py
tests/test_alleles.py
tests/test_aux_data.py
tests/test_bam_util.py
tests/test_barcodeFileParser.py
tests/test_blockzip.py
tests/test_countTable.py
tests/test_demultiplexing.py
tests/test_features.py
tests/test_fragment.py
tests/test_methylation.py
tests/test_molecule.py
tests/test_region_count.py
tests/test_tagger.py
tests/test_taps.py