SingleCellMultiOmics
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SingleCellMultiOmics
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__eq__() (singlecellmultiomics.fragment.fragment.Fragment method)
__finalise__() (singlecellmultiomics.molecule.molecule.Molecule method)
__getitem__() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
(singlecellmultiomics.utils.blockzip.BlockZip method)
__iter__() (singlecellmultiomics.fastqProcessing.fastqIterator.FastqIterator method)
(singlecellmultiomics.molecule.molecule.Molecule method)
(singlecellmultiomics.utils.blockzip.BlockZip method)
__len__() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
__next__() (singlecellmultiomics.fastqProcessing.fastqIterator.FastqIterator method)
A
add_fragment() (singlecellmultiomics.molecule.molecule.Molecule method)
add_readgroups_to_header() (in module singlecellmultiomics.bamProcessing.bamFunctions)
addAlleleInfo() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
addAlleleInfoOneBased() (singlecellmultiomics.alleleTools.alleleTools.AlleleResolver method)
addBarcode() (singlecellmultiomics.barcodeFileParser.barcodeFileParser.BarcodeParser method)
addFeature() (singlecellmultiomics.features.features.FeatureContainer method)
addSite() (singlecellmultiomics.universalBamTagger.mspjI.MSPJIFlagger method)
(singlecellmultiomics.universalBamTagger.nlaIII.NlaIIIFlagger method)
(singlecellmultiomics.universalBamTagger.scar.ScarFlagger method)
(singlecellmultiomics.universalBamTagger.scchic.ChicSeqFlagger method)
(singlecellmultiomics.universalBamTagger.tag.TagFlagger method)
addTagByTag() (singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord method)
addVariant() (singlecellmultiomics.features.features.FeatureContainer method)
AlleleHistogram (class in singlecellmultiomics.statistic.allele)
AlleleResolver (class in singlecellmultiomics.alleleTools.alleleTools)
AlleleTagger (class in singlecellmultiomics.universalBamTagger.universalBamTagger)
annotate() (singlecellmultiomics.molecule.featureannotatedmolecule.FeatureAnnotatedMolecule method)
AnnotatedCHICMolecule (class in singlecellmultiomics.molecule.chic)
AnnotatedNLAIIIMolecule (class in singlecellmultiomics.molecule.nlaIII)
AnnotatedTAPSCHICMolecule (class in singlecellmultiomics.molecule.taps)
AnnotatedTAPSNlaIIIMolecule (class in singlecellmultiomics.molecule.taps)
annotateUTRs() (singlecellmultiomics.features.features.FeatureContainer method)
appendTag() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
asFastq() (singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord method)
asIlluminaHeader() (singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord method)
assignment_function() (singlecellmultiomics.universalBamTagger.universalBamTagger.MoleculeIterator_OLD method)
(singlecellmultiomics.universalBamTagger.universalBamTagger.TranscriptIterator method)
assignReads() (in module singlecellmultiomics.bamProcessing.bamToCountTable)
B
bam_to_histogram() (in module singlecellmultiomics.bamProcessing.bamFeatureDensityVisualisation)
BarcodeParser (class in singlecellmultiomics.barcodeFileParser.barcodeFileParser)
base_calling_matrix_to_df() (in module singlecellmultiomics.molecule.consensus)
Base_RestrictionBisulfiteDemuxMethod (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.restrictionbisulfite)
bin_to_sort_value() (in module singlecellmultiomics.countTableProcessing.correct_count_table_bias)
BlockZip (class in singlecellmultiomics.utils.blockzip)
C
cache_size (singlecellmultiomics.molecule.molecule.Molecule attribute)
can_be_yielded() (singlecellmultiomics.molecule.molecule.Molecule method)
cell_counts_to_dataframe() (singlecellmultiomics.statistic.plate.PlateStatistic method)
CellReadCount (class in singlecellmultiomics.statistic.cellreadcount)
CELSeq1_c8_u4 (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq1)
CELSeq2_c8_u6 (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2)
CELSeq2_c8_u6_swapped_reads (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2)
CELSeq2_c8_u8 (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2)
CELSeq2_c8_u8_NNLAIII (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2)
check_variants() (singlecellmultiomics.molecule.molecule.Molecule method)
CHICFragment (class in singlecellmultiomics.fragment.chic)
CHICMolecule (class in singlecellmultiomics.molecule.chic)
ChicSeqFlagger (class in singlecellmultiomics.universalBamTagger.scchic)
chromosome (singlecellmultiomics.molecule.molecule.Molecule attribute)
clean_vcf_name() (singlecellmultiomics.alleleTools.alleleTools.AlleleResolver method)
close() (singlecellmultiomics.fastqProcessing.fastqHandle.FastqHandle method)
(singlecellmultiomics.pyutils.handlelimiter.HandleLimiter method)
complement (in module singlecellmultiomics.tagtools.tagtools)
complement() (in module singlecellmultiomics.utils.sequtils)
contains_valid_fragment() (singlecellmultiomics.molecule.molecule.Molecule method)
ConversionMatrix (class in singlecellmultiomics.statistic.conversions)
coordinate_to_bins() (in module singlecellmultiomics.bamProcessing.bamToCountTable)
(in module singlecellmultiomics.utils.binning)
coordinate_to_sliding_bin_locations() (in module singlecellmultiomics.bamProcessing.bamToCountTable)
(in module singlecellmultiomics.utils.binning)
create_count_table() (in module singlecellmultiomics.bamProcessing.bamToCountTable)
create_MD_tag() (in module singlecellmultiomics.utils.sequtils)
cstr() (in module singlecellmultiomics.bamProcessing.alignment_view)
CustomAssingmentQueryNameFlagger (class in singlecellmultiomics.universalBamTagger.customreads)
D
DataTypeHistogram (class in singlecellmultiomics.statistic.datatype)
debugMsg() (singlecellmultiomics.features.features.FeatureContainer method)
decodeKvPairs() (in module singlecellmultiomics.features.exonGTFtoIntronGTF)
deduplicate_to_single() (singlecellmultiomics.molecule.molecule.Molecule method)
deduplicate_to_single_CIGAR_spaced() (singlecellmultiomics.molecule.molecule.Molecule method)
deduplicate_to_single_CIGAR_spaced_from_dict() (singlecellmultiomics.molecule.molecule.Molecule method)
demultiplex() (singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.DemultiplexingStrategy method)
(singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.IlluminaBaseDemultiplexer method)
(singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod method)
(singlecellmultiomics.modularDemultiplexer.demultiplexModules.BULK_ILLUMINA.IlluminaBaseDemultiplexer method)
(singlecellmultiomics.modularDemultiplexer.demultiplexModules.Hexamer.HexamerBaseDemultiplexer method)
(singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII.NLAIII_384w_c8_u3 method)
(singlecellmultiomics.modularDemultiplexer.demultiplexModules.restrictionbisulfite.Base_RestrictionBisulfiteDemuxMethod method)
(singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC.SCCHIC_384w_c8_u3 method)
(singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader.DemultiplexingStrategyLoader method)
DemultiplexingStrategy (class in singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods)
DemultiplexingStrategyLoader (class in singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader)
detect() (singlecellmultiomics.libraryDetection.sequencingLibraryListing.SequencingLibraryLister method)
detect_alleles() (in module singlecellmultiomics.molecule.molecule)
detectLibYields() (singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader.DemultiplexingStrategyLoader method)
digest() (singlecellmultiomics.universalBamTagger.customreads.CustomAssingmentQueryNameFlagger method)
(singlecellmultiomics.universalBamTagger.customreads.VaninsbergheQueryNameFlagger method)
(singlecellmultiomics.universalBamTagger.mspjI.MSPJIFlagger method)
(singlecellmultiomics.universalBamTagger.nlaIII.NlaIIIFlagger method)
(singlecellmultiomics.universalBamTagger.rna.RNA_Flagger method)
(singlecellmultiomics.universalBamTagger.scar.ScarFlagger method)
(singlecellmultiomics.universalBamTagger.scchic.ChicSeqFlagger method)
(singlecellmultiomics.universalBamTagger.tag.TagFlagger method)
(singlecellmultiomics.universalBamTagger.taps.TAPSFlagger method)
(singlecellmultiomics.universalBamTagger.universalBamTagger.AlleleTagger method)
(singlecellmultiomics.universalBamTagger.universalBamTagger.QueryNameFlagger method)
DigestFlagger (class in singlecellmultiomics.universalBamTagger.digest)
distance_to_feature_start() (in module singlecellmultiomics.bamProcessing.bamFeatureDensityVisualisation)
distance_to_hit() (in module singlecellmultiomics.bamProcessing.bamFeatureDensityVisualisation)
downsampleDataFrame() (in module singlecellmultiomics.countTableProcessing.downsampleDataFrame)
downsampleRow() (in module singlecellmultiomics.countTableProcessing.downsampleDataFrame)
E
eq_function() (singlecellmultiomics.universalBamTagger.universalBamTagger.MoleculeIterator_OLD method)
exonGTF_to_intronGTF() (in module singlecellmultiomics.features.exonGTFtoIntronGTF)
expand() (singlecellmultiomics.barcodeFileParser.barcodeFileParser.BarcodeParser method)
expand_old() (singlecellmultiomics.barcodeFileParser.barcodeFileParser.BarcodeParser method)
extract_stretch_from_dict() (singlecellmultiomics.molecule.molecule.Molecule method)
F
FastqHandle (class in singlecellmultiomics.fastqProcessing.fastqHandle)
fastqHeaderSafeQualitiesToPhred() (in module singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods)
FastqIterator (class in singlecellmultiomics.fastqProcessing.fastqIterator)
FastqRecord (class in singlecellmultiomics.fastqProcessing.fastqIterator)
FeatureAnnotatedMolecule (class in singlecellmultiomics.molecule.featureannotatedmolecule)
FeatureContainer (class in singlecellmultiomics.features.features)
FeatureCountsSingleEndFragment (class in singlecellmultiomics.fragment.fragment)
fetchChromosome() (singlecellmultiomics.alleleTools.alleleTools.AlleleResolver method)
find_ranges() (in module singlecellmultiomics.utils.iteration)
findFeaturesAt (singlecellmultiomics.features.features.FeatureContainer attribute)
findFeaturesAtPysamAlign() (singlecellmultiomics.features.features.FeatureContainer method)
findFeaturesBetween() (singlecellmultiomics.features.features.FeatureContainer method)
findFeaturesBetweenBRK() (singlecellmultiomics.features.features.FeatureContainer method)
findNearestFeature (singlecellmultiomics.features.features.FeatureContainer attribute)
findNearestLeftFeature() (singlecellmultiomics.features.features.FeatureContainer method)
findNearestRightFeature() (singlecellmultiomics.features.features.FeatureContainer method)
finish_bam() (in module singlecellmultiomics.universalBamTagger.tapsTabulator)
formatColor() (in module singlecellmultiomics.libraryDetection.sequencingLibraryListing)
FourThiouridine (class in singlecellmultiomics.molecule.fourthiouridine)
fqSafe() (in module singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods)
Fraction (class in singlecellmultiomics.universalBamTagger.tapsTagger)
Fragment (class in singlecellmultiomics.fragment.fragment)
fragments (singlecellmultiomics.molecule.molecule.Molecule attribute)
FragmentSizeHistogram (class in singlecellmultiomics.statistic.fragmentsize)
FragmentWithoutUMI (class in singlecellmultiomics.fragment.fragment)
fromRawFastq() (singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord method)
fromTaggedBamRecord() (singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord method)
fromTaggedFastq() (singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord method)
G
GATK_indel_realign() (in module singlecellmultiomics.bamProcessing.bamFunctions)
generate_introns() (in module singlecellmultiomics.features.exonGTFtoIntronGTF)
get() (singlecellmultiomics.universalBamTagger.digest.RangeCache method)
get_a_reference_id() (singlecellmultiomics.molecule.molecule.Molecule method)
get_aligned_blocks() (singlecellmultiomics.molecule.molecule.Molecule method)
get_aligned_reference_bases_dict() (singlecellmultiomics.molecule.molecule.Molecule method)
get_alignment_stats() (singlecellmultiomics.molecule.molecule.Molecule method)
get_alignment_tensor() (singlecellmultiomics.molecule.molecule.Molecule method)
get_allele() (singlecellmultiomics.molecule.molecule.Molecule method)
get_barcode_sequences() (singlecellmultiomics.molecule.molecule.Molecule method)
get_base_calling_feature_matrix() (singlecellmultiomics.molecule.molecule.Molecule method)
get_base_calling_feature_matrix_spaced (singlecellmultiomics.molecule.molecule.Molecule attribute)
get_base_calling_training_data() (singlecellmultiomics.molecule.molecule.Molecule method)
get_base_observation_dict() (singlecellmultiomics.molecule.molecule.Molecule method)
get_base_observation_dict_NOREF() (singlecellmultiomics.molecule.molecule.Molecule method)
get_cached_fragment_count() (singlecellmultiomics.universalBamTagger.universalBamTagger.MoleculeIterator_OLD method)
get_CIGAR() (singlecellmultiomics.molecule.molecule.Molecule method)
get_consensus() (singlecellmultiomics.molecule.molecule.Molecule method)
get_consensus_base() (singlecellmultiomics.molecule.molecule.Molecule method)
get_consensus_base_frequencies() (singlecellmultiomics.molecule.molecule.Molecule method)
get_consensus_gc_ratio() (singlecellmultiomics.molecule.molecule.Molecule method)
get_consensus_read() (singlecellmultiomics.molecule.molecule.Molecule method)
get_consensus_training_data() (in module singlecellmultiomics.molecule.consensus)
get_contig_list_from_fasta() (in module singlecellmultiomics.utils.sequtils)
get_cut_site() (singlecellmultiomics.molecule.molecule.Molecule method)
get_df() (singlecellmultiomics.statistic.conversions.ConversionMatrix method)
(singlecellmultiomics.statistic.mappingquality.MappingQualityHistogram method)
(singlecellmultiomics.statistic.methylation.MethylationContextHistogram method)
(singlecellmultiomics.statistic.readcount.ReadCount method)
get_feature_vector() (singlecellmultiomics.molecule.molecule.Molecule method)
get_fragment_chromosome() (singlecellmultiomics.universalBamTagger.universalBamTagger.MoleculeIterator_OLD method)
get_fragment_span_sequence() (singlecellmultiomics.molecule.chic.CHICMolecule method)
(singlecellmultiomics.molecule.nlaIII.NlaIIIMolecule method)
get_gene_id_to_gene_name_conversion_table() (in module singlecellmultiomics.features.features)
get_hit_df() (singlecellmultiomics.molecule.featureannotatedmolecule.FeatureAnnotatedMolecule method)
get_html() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
get_match_mismatch_frequency() (singlecellmultiomics.molecule.molecule.Molecule method)
get_max_mapping_qual() (singlecellmultiomics.molecule.molecule.Molecule method)
get_mean_base_quality() (singlecellmultiomics.molecule.molecule.Molecule method)
get_mean_mapping_qual() (singlecellmultiomics.molecule.molecule.Molecule method)
get_mean_rt_fragment_size() (singlecellmultiomics.molecule.molecule.Molecule method)
get_methylated_count() (singlecellmultiomics.molecule.molecule.Molecule method)
get_methylation_dict() (singlecellmultiomics.molecule.molecule.Molecule method)
get_molecule_cache_size() (singlecellmultiomics.molecule.iterator.MoleculeIterator method)
get_R1() (singlecellmultiomics.fragment.fragment.Fragment method)
get_R2() (singlecellmultiomics.fragment.fragment.Fragment method)
get_random_primer_hash() (singlecellmultiomics.fragment.fragment.Fragment method)
get_random_primer_histogram() (in module singlecellmultiomics.bamProcessing.bamExtractRandomPrimerStats)
get_raw_barcode_sequences() (singlecellmultiomics.molecule.molecule.Molecule method)
get_read_group() (singlecellmultiomics.fragment.fragment.Fragment method)
get_reference_from_pysam_alignmentFile() (in module singlecellmultiomics.bamProcessing.bamFunctions)
get_reference_path_from_bam() (in module singlecellmultiomics.bamProcessing.bamFunctions)
get_rt_reaction_fragment_sizes() (singlecellmultiomics.molecule.molecule.Molecule method)
get_rt_reactions() (singlecellmultiomics.molecule.molecule.Molecule method)
get_safely_aligned_length() (singlecellmultiomics.molecule.molecule.Molecule method)
get_sample() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
get_site_location() (singlecellmultiomics.fragment.chic.CHICFragment method)
(singlecellmultiomics.fragment.nlaIII.NLAIIIFragment method)
get_span() (singlecellmultiomics.fragment.fragment.Fragment method)
get_strand() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
get_strand_repr() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
get_tag_counter() (singlecellmultiomics.molecule.molecule.Molecule method)
get_umi() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
get_umi_error_rate() (singlecellmultiomics.molecule.molecule.Molecule method)
get_undigested_site_count() (singlecellmultiomics.fragment.nlaIII.NLAIIIFragment method)
(singlecellmultiomics.molecule.nlaIII.NlaIIIMolecule method)
get_variant_phase() (in module singlecellmultiomics.molecule.molecule)
getAllele() (singlecellmultiomics.alleleTools.alleleTools.AlleleResolver method)
getAllelesAt() (singlecellmultiomics.alleleTools.alleleTools.AlleleResolver method)
getAutodetectStrategies() (singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader.DemultiplexingStrategyLoader method)
getBarcodeMapping() (singlecellmultiomics.barcodeFileParser.barcodeFileParser.BarcodeParser method)
getCentroids() (singlecellmultiomics.features.features.FeatureContainer method)
getCoverageAllPositions() (in module singlecellmultiomics.tagtools.tagtools)
getCycleOffset() (in module singlecellmultiomics.tagtools.tagtools)
getDemultiplexingSelectedStrategies() (singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader.DemultiplexingStrategyLoader method)
getIndexCorrectedBarcodeAndHammingDistance() (singlecellmultiomics.barcodeFileParser.barcodeFileParser.BarcodeParser method)
getListAllPositions() (in module singlecellmultiomics.tagtools.tagtools)
getMateDictSpanningCoordinates() (in module singlecellmultiomics.tagtools.tagtools)
getPairGenomicLocations() (in module singlecellmultiomics.tagtools.tagtools)
getParserSummary() (singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.DemultiplexingStrategy method)
getRandomPrimerHash() (in module singlecellmultiomics.tagtools.tagtools)
getReadTotalCycles() (in module singlecellmultiomics.tagtools.tagtools)
getReferenceList() (singlecellmultiomics.features.features.FeatureContainer method)
getSelectedStrategiesFromStringList() (singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader.DemultiplexingStrategyLoader method)
getSources() (in module singlecellmultiomics.tagtools.tagtools)
getTargetCount() (singlecellmultiomics.barcodeFileParser.barcodeFileParser.BarcodeParser method)
getTotalConsumption() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
getUniqueRandomPrimers() (in module singlecellmultiomics.tagtools.tagtools)
getWithinRange() (singlecellmultiomics.universalBamTagger.digest.RangeCache method)
H
hamming_circle() (in module singlecellmultiomics.barcodeFileParser.barcodeFileParser)
hamming_distance() (in module singlecellmultiomics.utils.sequtils)
HandleLimiter (class in singlecellmultiomics.pyutils.handlelimiter)
has_R1() (singlecellmultiomics.fragment.fragment.Fragment method)
has_R2() (singlecellmultiomics.fragment.fragment.Fragment method)
has_tag() (singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord method)
has_valid_span() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
header (singlecellmultiomics.fastqProcessing.fastqIterator.FastqRecord attribute)
HexamerBaseDemultiplexer (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.Hexamer)
human_readable() (in module singlecellmultiomics.statistic.plate)
I
identify_gene() (singlecellmultiomics.fragment.fragment.FeatureCountsSingleEndFragment method)
identify_site() (singlecellmultiomics.fragment.chic.CHICFragment method)
(singlecellmultiomics.fragment.nlaIII.NLAIIIFragment method)
identify_strand() (singlecellmultiomics.fragment.fragment.Fragment method)
IlluminaBaseDemultiplexer (class in singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods)
(class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.BULK_ILLUMINA)
increaseAndRecordOversequencing() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
is_main_chromosome() (in module singlecellmultiomics.utils.sequtils)
is_multimapped() (singlecellmultiomics.molecule.molecule.Molecule method)
is_valid() (singlecellmultiomics.fragment.chic.CHICFragment method)
(singlecellmultiomics.fragment.fragment.FeatureCountsSingleEndFragment method)
(singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.fragment.nlaIII.NLAIIIFragment method)
(singlecellmultiomics.molecule.chic.CHICMolecule method)
(singlecellmultiomics.molecule.fourthiouridine.FourThiouridine method)
(singlecellmultiomics.molecule.molecule.Molecule method)
(singlecellmultiomics.molecule.nlaIII.NlaIIIMolecule method)
(singlecellmultiomics.molecule.taps.AnnotatedTAPSCHICMolecule method)
(singlecellmultiomics.molecule.taps.AnnotatedTAPSNlaIIIMolecule method)
(singlecellmultiomics.molecule.taps.TAPSCHICMolecule method)
(singlecellmultiomics.molecule.taps.TAPSMolecule method)
(singlecellmultiomics.molecule.taps.TAPSNlaIIIMolecule method)
iter_reads() (singlecellmultiomics.molecule.molecule.Molecule method)
L
libraryReplace() (singlecellmultiomics.libraryDetection.sequencingLibraryListing.SequencingLibraryLister method)
list() (singlecellmultiomics.barcodeFileParser.barcodeFileParser.BarcodeParser method)
(singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader.DemultiplexingStrategyLoader method)
loadBED() (singlecellmultiomics.features.features.FeatureContainer method)
loadGTF() (singlecellmultiomics.features.features.FeatureContainer method)
loadSNPSFromVcf() (singlecellmultiomics.features.features.FeatureContainer method)
localisation_function() (singlecellmultiomics.universalBamTagger.universalBamTagger.MoleculeIterator_OLD method)
(singlecellmultiomics.universalBamTagger.universalBamTagger.TranscriptIterator method)
M
MapabilityReader (class in singlecellmultiomics.bamProcessing.bamFunctions)
mappability() (singlecellmultiomics.statistic.readcount.ReadCount method)
MappingQualityHistogram (class in singlecellmultiomics.statistic.mappingquality)
massIdConvert() (in module singlecellmultiomics.features.features)
meanOfCounter() (in module singlecellmultiomics.pyutils.pyutils)
metaFromRead() (in module singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods)
MethylationContextHistogram (class in singlecellmultiomics.statistic.methylation)
might_be_variant (in module singlecellmultiomics.molecule.molecule)
Molecule (class in singlecellmultiomics.molecule.molecule)
molecule_iterator_filter() (in module singlecellmultiomics.molecule.filter)
molecule_to_context_call_dict() (singlecellmultiomics.molecule.taps.TAPS method)
molecule_to_random_primer_dict() (in module singlecellmultiomics.molecule.molecule)
(in module singlecellmultiomics.universalBamTagger.universalBamTagger)
MoleculeIterator (class in singlecellmultiomics.molecule.iterator)
MoleculeIterator_OLD (class in singlecellmultiomics.universalBamTagger.universalBamTagger)
MSPJI_c8_u3 (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.MSPJI)
MSPJIFlagger (class in singlecellmultiomics.universalBamTagger.mspjI)
N
Nla_384w_u8_c8_ad3_is15 (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.restrictionbisulfite)
NLAIII_384w_c8_u3 (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII)
NLAIII_96w_c8_u3 (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII)
nlaIII_molecule_acceptance_function() (in module singlecellmultiomics.bamProcessing.bamPlotRTstats)
NlaIIIFlagger (class in singlecellmultiomics.universalBamTagger.nlaIII)
NLAIIIFragment (class in singlecellmultiomics.fragment.nlaIII)
NlaIIIMolecule (class in singlecellmultiomics.molecule.nlaIII)
NonMultiplexable
O
obtain_approximate_reference_cut_position() (in module singlecellmultiomics.bamProcessing.bamToMethylationAndCopyNumber)
obtain_conversions() (singlecellmultiomics.molecule.fourthiouridine.FourThiouridine method)
obtain_methylation_calls() (singlecellmultiomics.molecule.taps.TAPSMolecule method)
obtain_variant_statistics() (in module singlecellmultiomics.bamProcessing.variantStats)
OversequencingHistogram (class in singlecellmultiomics.statistic.oversequencing)
P
phred_to_prob() (in module singlecellmultiomics.utils.sequtils)
phredToFastqHeaderSafeQualities() (in module singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods)
PlateStatistic (class in singlecellmultiomics.statistic.plate)
plot() (singlecellmultiomics.statistic.allele.AlleleHistogram method)
(singlecellmultiomics.statistic.cellreadcount.CellReadCount method)
(singlecellmultiomics.statistic.conversions.ConversionMatrix method)
(singlecellmultiomics.statistic.datatype.DataTypeHistogram method)
(singlecellmultiomics.statistic.fragmentsize.FragmentSizeHistogram method)
(singlecellmultiomics.statistic.mappingquality.MappingQualityHistogram method)
(singlecellmultiomics.statistic.methylation.MethylationContextHistogram method)
(singlecellmultiomics.statistic.oversequencing.OversequencingHistogram method)
(singlecellmultiomics.statistic.plate.PlateStatistic method)
(singlecellmultiomics.statistic.readcount.ReadCount method)
(singlecellmultiomics.statistic.rejectionreasons.RejectionReasonHistogram method)
(singlecellmultiomics.statistic.scchicligation.ScCHICLigation method)
(singlecellmultiomics.statistic.tag.TagHistogram method)
plus (singlecellmultiomics.fastqProcessing.fastqIterator.FastqRecord attribute)
position_to_context() (singlecellmultiomics.molecule.taps.TAPS method)
processRead() (singlecellmultiomics.statistic.allele.AlleleHistogram method)
(singlecellmultiomics.statistic.cellreadcount.CellReadCount method)
(singlecellmultiomics.statistic.conversions.ConversionMatrix method)
(singlecellmultiomics.statistic.datatype.DataTypeHistogram method)
(singlecellmultiomics.statistic.fragmentsize.FragmentSizeHistogram method)
(singlecellmultiomics.statistic.mappingquality.MappingQualityHistogram method)
(singlecellmultiomics.statistic.methylation.MethylationContextHistogram method)
(singlecellmultiomics.statistic.oversequencing.OversequencingHistogram method)
(singlecellmultiomics.statistic.plate.PlateStatistic method)
(singlecellmultiomics.statistic.readcount.ReadCount method)
(singlecellmultiomics.statistic.rejectionreasons.RejectionReasonHistogram method)
(singlecellmultiomics.statistic.scchicligation.ScCHICLigation method)
(singlecellmultiomics.statistic.statistic.Statistic method)
(singlecellmultiomics.statistic.tag.TagHistogram method)
(singlecellmultiomics.statistic.trimming.TrimmingStats method)
prune() (singlecellmultiomics.pyutils.handlelimiter.HandleLimiter method)
purge() (singlecellmultiomics.universalBamTagger.digest.RangeCache method)
Q
qual (singlecellmultiomics.fastqProcessing.fastqIterator.FastqRecord attribute)
QueryNameFlagger (class in singlecellmultiomics.universalBamTagger.universalBamTagger)
R
RangeCache (class in singlecellmultiomics.universalBamTagger.digest)
read_cached() (singlecellmultiomics.alleleTools.alleleTools.AlleleResolver method)
read_contig_to_cache() (singlecellmultiomics.utils.blockzip.BlockZip method)
read_file_line() (singlecellmultiomics.utils.blockzip.BlockZip method)
read_has_alternative_hits_to_non_alts() (in module singlecellmultiomics.bamProcessing.bamToCountTable)
read_should_be_counted() (in module singlecellmultiomics.bamProcessing.bamToCountTable)
ReadCount (class in singlecellmultiomics.statistic.readcount)
ReadCycleIterator (class in singlecellmultiomics.tagtools.tagtools)
readIsDuplicate() (in module singlecellmultiomics.statistic.cellreadcount)
(in module singlecellmultiomics.statistic.fragmentsize)
readTag() (in module singlecellmultiomics.bamProcessing.bamToCountTable)
reference (singlecellmultiomics.molecule.molecule.Molecule attribute)
RejectionReasonHistogram (class in singlecellmultiomics.statistic.rejectionreasons)
reverse_complement() (in module singlecellmultiomics.utils.sequtils)
reverseComplement() (in module singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods)
RNA_Flagger (class in singlecellmultiomics.universalBamTagger.rna)
run_multiome_tagging() (in module singlecellmultiomics.universalBamTagger.bamtagmultiome)
run_multiome_tagging_cmd() (in module singlecellmultiomics.universalBamTagger.bamtagmultiome)
S
sample_assignment_function() (singlecellmultiomics.universalBamTagger.universalBamTagger.MoleculeIterator_OLD method)
SamTag (class in singlecellmultiomics.tags.tags)
ScarFlagger (class in singlecellmultiomics.universalBamTagger.scar)
ScartraceR1 (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.scartrace)
ScartraceR2 (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.scartrace)
SCCHIC_384w_c8_u3 (class in singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC)
ScCHICLigation (class in singlecellmultiomics.statistic.scchicligation)
select_bam_file() (in module singlecellmultiomics.libraryProcessing.libraryStatistics)
select_fastq_file() (in module singlecellmultiomics.libraryProcessing.libraryStatistics)
selectedStrategiesBasedOnYield() (singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader.DemultiplexingStrategyLoader method)
sequence (singlecellmultiomics.fastqProcessing.fastqIterator.FastqRecord attribute)
SequencingLibraryLister (class in singlecellmultiomics.libraryDetection.sequencingLibraryListing)
set() (singlecellmultiomics.universalBamTagger.digest.RangeCache method)
set_duplicate() (singlecellmultiomics.fragment.fragment.Fragment method)
set_intron_exon_features() (singlecellmultiomics.molecule.featureannotatedmolecule.FeatureAnnotatedMolecule method)
set_meta() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
set_methylation_call_tags() (singlecellmultiomics.molecule.molecule.Molecule method)
set_recognized_sequence() (singlecellmultiomics.fragment.fragment.Fragment method)
set_rejection_reason() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
set_sample() (singlecellmultiomics.fragment.fragment.Fragment method)
set_site() (singlecellmultiomics.fragment.chic.CHICFragment method)
(singlecellmultiomics.fragment.nlaIII.NLAIIIFragment method)
set_spliced() (singlecellmultiomics.molecule.featureannotatedmolecule.FeatureAnnotatedMolecule method)
set_strand() (singlecellmultiomics.fragment.fragment.Fragment method)
set_umi() (singlecellmultiomics.fragment.fragment.FragmentWithoutUMI method)
setAllele() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
setFragmentSize() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
setFragmentTrust() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
setLigationSite() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
setRandomPrimer() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
setRawDemuxCount() (singlecellmultiomics.statistic.readcount.ReadCount method)
setRawReadCount() (singlecellmultiomics.statistic.readcount.ReadCount method)
setRecognizedSequence() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
setRejectionReason() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
setSiteCoordinate() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
setSiteOversequencing() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
setSource() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
setStrand() (singlecellmultiomics.universalBamTagger.digest.DigestFlagger method)
singlecellmultiomics (module)
singlecellmultiomics.alleleTools (module)
singlecellmultiomics.alleleTools.alleleTools (module)
singlecellmultiomics.bamProcessing (module)
singlecellmultiomics.bamProcessing.alignment_view (module)
singlecellmultiomics.bamProcessing.bamDuprate (module)
singlecellmultiomics.bamProcessing.bamExtractRandomPrimerStats (module)
singlecellmultiomics.bamProcessing.bamFeatureDensityVisualisation (module)
singlecellmultiomics.bamProcessing.bamFilter (module)
singlecellmultiomics.bamProcessing.bamFunctions (module)
singlecellmultiomics.bamProcessing.bamMappingRate (module)
singlecellmultiomics.bamProcessing.bamPlateVisualisation (module)
singlecellmultiomics.bamProcessing.bamPlotRTstats (module)
singlecellmultiomics.bamProcessing.bamTabulator (module)
singlecellmultiomics.bamProcessing.bamToCountTable (module)
singlecellmultiomics.bamProcessing.bamToMethylationAndCopyNumber (module)
singlecellmultiomics.bamProcessing.variantStats (module)
singlecellmultiomics.barcodeFileParser (module)
singlecellmultiomics.barcodeFileParser.barcodeFileParser (module)
singlecellmultiomics.countTableProcessing (module)
singlecellmultiomics.countTableProcessing.correct_count_table_bias (module)
singlecellmultiomics.countTableProcessing.downsampleDataFrame (module)
singlecellmultiomics.fastaProcessing (module)
singlecellmultiomics.fastaProcessing.createMapabilityIndex (module)
singlecellmultiomics.fastaProcessing.fastaMaskVariants (module)
singlecellmultiomics.fastqProcessing (module)
singlecellmultiomics.fastqProcessing.fastqHandle (module)
singlecellmultiomics.fastqProcessing.fastqIterator (module)
singlecellmultiomics.features (module)
singlecellmultiomics.features.exonGTFtoIntronGTF (module)
singlecellmultiomics.features.features (module)
singlecellmultiomics.fragment (module)
singlecellmultiomics.fragment.chic (module)
singlecellmultiomics.fragment.fragment (module)
singlecellmultiomics.fragment.nlaIII (module)
singlecellmultiomics.libraryDetection (module)
singlecellmultiomics.libraryDetection.archivestats (module)
singlecellmultiomics.libraryDetection.sequencingLibraryListing (module)
singlecellmultiomics.libraryProcessing (module)
singlecellmultiomics.libraryProcessing.libraryStatistics (module)
singlecellmultiomics.modularDemultiplexer (module)
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods (module)
singlecellmultiomics.modularDemultiplexer.demultiplexedFastqConversion (module)
singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader (module)
singlecellmultiomics.modularDemultiplexer.demultiplexModules (module)
singlecellmultiomics.modularDemultiplexer.demultiplexModules.BULK_ILLUMINA (module)
singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq1 (module)
singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2 (module)
singlecellmultiomics.modularDemultiplexer.demultiplexModules.Hexamer (module)
singlecellmultiomics.modularDemultiplexer.demultiplexModules.MSPJI (module)
singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII (module)
singlecellmultiomics.modularDemultiplexer.demultiplexModules.restrictionbisulfite (module)
singlecellmultiomics.modularDemultiplexer.demultiplexModules.scartrace (module)
singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC (module)
singlecellmultiomics.modularDemultiplexer.demux (module)
singlecellmultiomics.molecule (module)
singlecellmultiomics.molecule.chic (module)
singlecellmultiomics.molecule.consensus (module)
singlecellmultiomics.molecule.featureannotatedmolecule (module)
singlecellmultiomics.molecule.filter (module)
singlecellmultiomics.molecule.fourthiouridine (module)
singlecellmultiomics.molecule.iterator (module)
singlecellmultiomics.molecule.molecule (module)
singlecellmultiomics.molecule.nlaIII (module)
singlecellmultiomics.molecule.rna (module)
singlecellmultiomics.molecule.taps (module)
singlecellmultiomics.pyutils (module)
singlecellmultiomics.pyutils.handlelimiter (module)
singlecellmultiomics.pyutils.pyutils (module)
singlecellmultiomics.statistic (module)
singlecellmultiomics.statistic.allele (module)
singlecellmultiomics.statistic.cellreadcount (module)
singlecellmultiomics.statistic.conversions (module)
singlecellmultiomics.statistic.datatype (module)
singlecellmultiomics.statistic.fragmentsize (module)
singlecellmultiomics.statistic.mappingquality (module)
singlecellmultiomics.statistic.methylation (module)
singlecellmultiomics.statistic.oversequencing (module)
singlecellmultiomics.statistic.plate (module)
singlecellmultiomics.statistic.readcount (module)
singlecellmultiomics.statistic.rejectionreasons (module)
singlecellmultiomics.statistic.scchicligation (module)
singlecellmultiomics.statistic.statistic (module)
singlecellmultiomics.statistic.tag (module)
singlecellmultiomics.statistic.trimming (module)
singlecellmultiomics.tags (module)
singlecellmultiomics.tags.tags (module)
singlecellmultiomics.tags.write_tags_md (module)
singlecellmultiomics.tagtools (module)
singlecellmultiomics.tagtools.tagtools (module)
singlecellmultiomics.universalBamTagger (module)
singlecellmultiomics.universalBamTagger.4SUtagger (module)
singlecellmultiomics.universalBamTagger.bamtagmultiome (module)
singlecellmultiomics.universalBamTagger.customreads (module)
singlecellmultiomics.universalBamTagger.digest (module)
singlecellmultiomics.universalBamTagger.mspjI (module)
singlecellmultiomics.universalBamTagger.nlaIII (module)
singlecellmultiomics.universalBamTagger.rna (module)
singlecellmultiomics.universalBamTagger.scar (module)
singlecellmultiomics.universalBamTagger.scchic (module)
singlecellmultiomics.universalBamTagger.tag (module)
singlecellmultiomics.universalBamTagger.taps (module)
singlecellmultiomics.universalBamTagger.tapsTabulator (module)
singlecellmultiomics.universalBamTagger.tapsTagger (module)
singlecellmultiomics.universalBamTagger.universalBamTagger (module)
singlecellmultiomics.utils (module)
singlecellmultiomics.utils.binning (module)
singlecellmultiomics.utils.blockzip (module)
singlecellmultiomics.utils.html (module)
singlecellmultiomics.utils.iteration (module)
singlecellmultiomics.utils.sequtils (module)
singlecellmultiomics.utils.submission (module)
singlecellmultiomics.version (module)
SingleEndTranscript (class in singlecellmultiomics.fragment.fragment)
site_is_mapable() (singlecellmultiomics.bamProcessing.bamFunctions.MapabilityReader method)
sort() (singlecellmultiomics.features.features.FeatureContainer method)
sort_and_index() (in module singlecellmultiomics.bamProcessing.bamFunctions)
sorted_bam_file() (in module singlecellmultiomics.bamProcessing.bamFunctions)
spanEnd (singlecellmultiomics.molecule.molecule.Molecule attribute)
spanStart (singlecellmultiomics.molecule.molecule.Molecule attribute)
split_nth() (in module singlecellmultiomics.utils.sequtils)
Statistic (class in singlecellmultiomics.statistic.statistic)
StatisticHistogram (class in singlecellmultiomics.statistic.statistic)
strand (singlecellmultiomics.molecule.molecule.Molecule attribute)
strategyYieldsToFormattedReport() (singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader.DemultiplexingStrategyLoader method)
style_str() (in module singlecellmultiomics.utils.html)
T
TagFlagger (class in singlecellmultiomics.universalBamTagger.tag)
TaggedRecord (class in singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods)
TagHistogram (class in singlecellmultiomics.statistic.tag)
tagPysamRead() (singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord method)
tagToHumanName() (in module singlecellmultiomics.bamProcessing.bamToCountTable)
TAPS (class in singlecellmultiomics.molecule.taps)
TAPSCHICMolecule (class in singlecellmultiomics.molecule.taps)
TAPSFlagger (class in singlecellmultiomics.universalBamTagger.taps)
TAPSMolecule (class in singlecellmultiomics.molecule.taps)
TAPSNlaIIIMolecule (class in singlecellmultiomics.molecule.taps)
to_csv() (singlecellmultiomics.statistic.cellreadcount.CellReadCount method)
(singlecellmultiomics.statistic.conversions.ConversionMatrix method)
(singlecellmultiomics.statistic.mappingquality.MappingQualityHistogram method)
(singlecellmultiomics.statistic.methylation.MethylationContextHistogram method)
(singlecellmultiomics.statistic.plate.PlateStatistic method)
(singlecellmultiomics.statistic.readcount.ReadCount method)
(singlecellmultiomics.statistic.scchicligation.ScCHICLigation method)
(singlecellmultiomics.statistic.statistic.StatisticHistogram method)
train_consensus_model() (in module singlecellmultiomics.molecule.consensus)
TranscriptIterator (class in singlecellmultiomics.universalBamTagger.universalBamTagger)
TrimmingStats (class in singlecellmultiomics.statistic.trimming)
U
umi_eq() (singlecellmultiomics.fragment.fragment.Fragment method)
UmiBarcodeDemuxMethod (class in singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods)
update_ligation_motif() (singlecellmultiomics.molecule.chic.CHICMolecule method)
update_mapability() (singlecellmultiomics.molecule.molecule.Molecule method)
update_span() (singlecellmultiomics.fragment.fragment.Fragment method)
update_umi() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
V
VaninsbergheQueryNameFlagger (class in singlecellmultiomics.universalBamTagger.customreads)
varianceOfCounter() (in module singlecellmultiomics.pyutils.pyutils)
VASA (class in singlecellmultiomics.molecule.rna)
verify_and_fix_bam() (in module singlecellmultiomics.bamProcessing.bamFunctions)
visualise_molecule() (in module singlecellmultiomics.bamProcessing.alignment_view)
W
wccount() (in module singlecellmultiomics.pyutils.pyutils)
wccountgz() (in module singlecellmultiomics.pyutils.pyutils)
write() (singlecellmultiomics.fastqProcessing.fastqHandle.FastqHandle method)
(singlecellmultiomics.pyutils.handlelimiter.HandleLimiter method)
(singlecellmultiomics.utils.blockzip.BlockZip method)
write_allele_phasing_information_tag() (singlecellmultiomics.molecule.molecule.Molecule method)
write_cache() (singlecellmultiomics.alleleTools.alleleTools.AlleleResolver method)
write_program_tag() (in module singlecellmultiomics.bamProcessing.bamFunctions)
write_pysam() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.molecule.Molecule method)
write_tags() (singlecellmultiomics.fragment.fragment.Fragment method)
(singlecellmultiomics.molecule.chic.AnnotatedCHICMolecule method)
(singlecellmultiomics.molecule.chic.CHICMolecule method)
(singlecellmultiomics.molecule.featureannotatedmolecule.FeatureAnnotatedMolecule method)
(singlecellmultiomics.molecule.molecule.Molecule method)
(singlecellmultiomics.molecule.nlaIII.AnnotatedNLAIIIMolecule method)
(singlecellmultiomics.molecule.nlaIII.NlaIIIMolecule method)
(singlecellmultiomics.molecule.taps.AnnotatedTAPSCHICMolecule method)
(singlecellmultiomics.molecule.taps.AnnotatedTAPSNlaIIIMolecule method)
(singlecellmultiomics.molecule.taps.TAPSCHICMolecule method)
(singlecellmultiomics.molecule.taps.TAPSNlaIIIMolecule method)
write_tags_to_psuedoreads() (singlecellmultiomics.molecule.molecule.Molecule method)
write_tensor() (singlecellmultiomics.fragment.fragment.Fragment method)
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