singlecellmultiomics.modularDemultiplexer.demultiplexModules package

Submodules

singlecellmultiomics.modularDemultiplexer.demultiplexModules.BULK_ILLUMINA module

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.BULK_ILLUMINA.IlluminaBaseDemultiplexer(indexFileParser, indexFileAlias='illumina_merged_ThruPlex48S_RP', **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.DemultiplexingStrategy

demultiplex(records, library=None, reason=None, **kwargs)[source]

singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq1 module

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq1.CELSeq1_c8_u4(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2 module

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2.CELSeq2_c8_u6(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2.CELSeq2_c8_u6_swapped_reads(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2.CELSeq2_c8_u8(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2.CELSeq2_c8_u8_NNLAIII(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

singlecellmultiomics.modularDemultiplexer.demultiplexModules.Hexamer module

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.Hexamer.HexamerBaseDemultiplexer(indexFileParser, illuminaIndicesAlias='illumina_merged_iPCR_RP', **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.DemultiplexingStrategy

demultiplex(records, library=None, **kwargs)[source]

singlecellmultiomics.modularDemultiplexer.demultiplexModules.MSPJI module

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.MSPJI.MSPJI_c8_u3(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII module

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII.NLAIII_384w_c8_u3(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

demultiplex(records, **kwargs)[source]
class singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII.NLAIII_96w_c8_u3(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

singlecellmultiomics.modularDemultiplexer.demultiplexModules.restrictionbisulfite module

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.restrictionbisulfite.Base_RestrictionBisulfiteDemuxMethod(umiRead=0, umiStart=0, umiLength=8, barcodeRead=0, barcodeStart=8, barcodeLength=8, enzymeRead=0, enzymeStart=16, enzymeLength=3, ispcrRead=0, ispcrStart=19, ispcrLength=15, ispcrSeq='CAGTGGTATCAGAGT', barcodeFileParser=None, barcodeFileAlias=None, indexFileParser=None, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

demultiplex(records, **kwargs)[source]
class singlecellmultiomics.modularDemultiplexer.demultiplexModules.restrictionbisulfite.Nla_384w_u8_c8_ad3_is15(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.demultiplexModules.restrictionbisulfite.Base_RestrictionBisulfiteDemuxMethod

singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC module

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC.SCCHIC_384w_c8_u3(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

demultiplex(records, **kwargs)[source]

singlecellmultiomics.modularDemultiplexer.demultiplexModules.scartrace module

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.scartrace.ScartraceR1(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

class singlecellmultiomics.modularDemultiplexer.demultiplexModules.scartrace.ScartraceR2(barcodeFileParser, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod

Module contents