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
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_NH
(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
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
-
class
singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII.
NLAIII_384w_c8_u3_SINGLE_END
(barcodeFileParser, **kwargs)[source]¶ Bases:
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod
-
class
singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII.
NLAIII_96w_c8_u3
(barcodeFileParser, **kwargs)[source]¶ Bases:
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod
-
class
singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII.
NLAIII_96w_c8_u3_SINGLE_END
(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
singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC module¶
-
class
singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC.
SCCHIC_384w_c8_u3
(barcodeFileParser, random_primer_read=1, random_primer_length=6, **kwargs)[source]¶ Bases:
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod
-
class
singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC.
SCCHIC_384w_c8_u3_cs2
(barcodeFileParser=None, indexFileParser=None, indexFileAlias='illumina_merged_ThruPlex48S_RP', **kwargs)[source]¶ Bases:
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.IlluminaBaseDemultiplexer
-
class
singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC.
SCCHIC_384w_c8_u3_direct_ligation
(barcodeFileParser, random_primer_read=None, random_primer_length=None, **kwargs)[source]¶ Bases:
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod
-
class
singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC.
SCCHIC_384w_c8_u3_direct_ligation_SINGLE_END
(barcodeFileParser, random_primer_read=None, random_primer_length=None, **kwargs)[source]¶ Bases:
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod
-
class
singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC.
SCCHIC_384w_c8_u3_pdt
(barcodeFileParser=None, indexFileParser=None, indexFileAlias='illumina_merged_ThruPlex48S_RP', **kwargs)[source]¶ Bases:
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.IlluminaBaseDemultiplexer
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
-
class
singlecellmultiomics.modularDemultiplexer.demultiplexModules.scartrace.
ScartraceR2RP4
(barcodeFileParser, **kwargs)[source]¶ Bases:
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod