singlecellmultiomics.statistic package

Submodules

singlecellmultiomics.statistic.allele module

class singlecellmultiomics.statistic.allele.AlleleHistogram(args)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

plot(target_path, title=None)[source]
processRead(R1, R2)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None

singlecellmultiomics.statistic.cellreadcount module

class singlecellmultiomics.statistic.cellreadcount.CellReadCount(args)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

plot(target_path, title=None)[source]
processRead(R1, R2=None)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None
to_csv(path)[source]
singlecellmultiomics.statistic.cellreadcount.readIsDuplicate(read)[source]

singlecellmultiomics.statistic.conversions module

class singlecellmultiomics.statistic.conversions.ConversionMatrix(args, process_reads=200000)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

get_df()[source]
plot(target_path, title=None)[source]
processRead(R1, R2)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None
to_csv(path)[source]

singlecellmultiomics.statistic.datatype module

class singlecellmultiomics.statistic.datatype.DataTypeHistogram(args)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

plot(target_path, title=None)[source]
processRead(R1, R2)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None

singlecellmultiomics.statistic.fragmentsize module

class singlecellmultiomics.statistic.fragmentsize.FragmentSizeHistogram(args)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

plot(target_path, title=None)[source]
processRead(R1, R2=None)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None
singlecellmultiomics.statistic.fragmentsize.readIsDuplicate(read)[source]

singlecellmultiomics.statistic.mappingquality module

class singlecellmultiomics.statistic.mappingquality.MappingQualityHistogram(args)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

get_df()[source]
plot(target_path, title=None)[source]
processRead(R1, R2)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None
to_csv(path)[source]

singlecellmultiomics.statistic.methylation module

class singlecellmultiomics.statistic.methylation.MethylationContextHistogram(args)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

get_df()[source]
plot(target_path, title=None)[source]
processRead(R1, R2)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None
to_csv(path)[source]

singlecellmultiomics.statistic.oversequencing module

class singlecellmultiomics.statistic.oversequencing.OversequencingHistogram(args)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

plot(target_path, title=None)[source]
processRead(R1, R2=None)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None

singlecellmultiomics.statistic.plate module

class singlecellmultiomics.statistic.plate.PlateStatistic(args)[source]

Bases: object

cell_counts_to_dataframe(cell_counts, mux, name='raw_reads')[source]
plot(target_path, title=None)[source]
processRead(R1, R2)[source]
to_csv(path)[source]
singlecellmultiomics.statistic.plate.human_readable(value, targetDigits=2, fp=0)[source]

singlecellmultiomics.statistic.readcount module

class singlecellmultiomics.statistic.readcount.ReadCount(args)[source]

Bases: singlecellmultiomics.statistic.statistic.Statistic

get_df()[source]
mappability()[source]
plot(target_path, title=None)[source]
processRead(R1, R2)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None
setRawDemuxCount(readCount, paired=True)[source]
setRawReadCount(readCount, paired=True)[source]
to_csv(path)[source]

singlecellmultiomics.statistic.rejectionreasons module

class singlecellmultiomics.statistic.rejectionreasons.RejectionReasonHistogram(args)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

plot(target_path, title=None)[source]
processRead(R1, R2)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None

singlecellmultiomics.statistic.scchicligation module

class singlecellmultiomics.statistic.scchicligation.ScCHICLigation(args)[source]

Bases: object

plot(target_path, title=None)[source]
processRead(R1, R2)[source]
to_csv(path)[source]

singlecellmultiomics.statistic.statistic module

class singlecellmultiomics.statistic.statistic.Statistic(args)[source]

Bases: object

Statistic object, initialised with arguments

Parameters:args (argparse object) –
processRead(R1, R2=None)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None
class singlecellmultiomics.statistic.statistic.StatisticHistogram(args)[source]

Bases: singlecellmultiomics.statistic.statistic.Statistic

to_csv(path)[source]

singlecellmultiomics.statistic.tag module

class singlecellmultiomics.statistic.tag.TagHistogram(args)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

plot(target_path, title=None)[source]
processRead(R1, R2=None)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None

singlecellmultiomics.statistic.trimming module

class singlecellmultiomics.statistic.trimming.TrimmingStats(args)[source]

Bases: singlecellmultiomics.statistic.statistic.StatisticHistogram

processRead(R1, R2=None)[source]

Update the statistic with information from READ

Parameters:read (PySAM Aligned segment) –
Returns:
Return type:None

Module contents