API

Import scReadSim as:

import scReadSim

Utility

scReadSim.Utility.CallPeak(macs3_directory, ...)	Perform peak calling using MACS3
scReadSim.Utility.ExtractBAMCoverage(...)	Examine the covered chromosome names for the input bam file.
scReadSim.Utility.scATAC_CreateFeatureSets(...)	Create the foreground and background feature set for the input scATAC-seq bam file.
scReadSim.Utility.scRNA_CreateFeatureSets(...)	Create the foreground and background feature set for the input scRNA-seq bam file.
scReadSim.Utility.countmat_mainloop(rec_id)	Construct count vector for each scATAC-seq feature.
scReadSim.Utility.scATAC_bam2countmat_paral(...)	Construct count matrix for scATAC-seq BAM file.
scReadSim.Utility.scRNA_UMIcountmat_mainloop(rec_id)	Construct count vector for each scRNA-seq feature.
scReadSim.Utility.scRNA_bam2countmat_paral(...)	Construct read (or UMI) count matrix for scRNA-seq BAM file.
scReadSim.Utility.scATAC_bam2countmat_OutputPeak(...)	Construct count matrix for task with user input features set.
scReadSim.Utility.find_nearest_peak(array, ...)	Find the index of largest-read-density input peak from array with a length similar to value.
scReadSim.Utility.find_nearest_nonpeak(...)	Find the index of largest-read-density input non-peak from array with a length similar to value.
scReadSim.Utility.match_peak(...)	Map from output peaks to input peaks according to the similarity of peak length.
scReadSim.Utility.match_nonpeak(...)	Map from output non-peaks to input non-peaks according to the similarity of peak length.
scReadSim.Utility.bam2MarginalCount(...)	Count read overlapped for each feature from input bed file.
scReadSim.Utility.FeatureMapping(...[, n_top])	Obtain mappings between input and output peaks, input and output non-peaks.
scReadSim.Utility.scATAC_bam2countmat_paral_MultiSample(...)	Multi-sample/replicate implement of scReadSim for constructing count matrices for scATAC-seq BAM file.
scReadSim.Utility.scRNA_bam2countmat_paral_MultiSample(...)	Multi-sample/replicate implement of scReadSim for constructing count matrices for scRNA-seq BAM file.

scATAC_GenerateBAM

scReadSim.scATAC_GenerateBAM.flatten(x)	Flatten a nested list.
scReadSim.scATAC_GenerateBAM.cellbarcode_generator(length)	Generate random cellbarcode.
scReadSim.scATAC_GenerateBAM.find_leftnearest_nonpeak(...)	Find the gray peak's left nearest non-peak from a non-peak list.
scReadSim.scATAC_GenerateBAM.scATAC_GenerateBAMCoord(...)	Generate Synthetic reads in BED format.
scReadSim.scATAC_GenerateBAM.scATAC_GenerateBAMCoord_OutputPeak(...)	Generate Synthetic reads in BED format.
scReadSim.scATAC_GenerateBAM.scATAC_CombineBED(...)	Combine the bed files of foreground and background feature sets into one bed file.
scReadSim.scATAC_GenerateBAM.scATAC_BED2FASTQ(...)	Convert Synthetic reads from BED to FASTQ.
scReadSim.scATAC_GenerateBAM.AlignSyntheticBam_Pair(...)	Convert Synthetic reads from FASTQ to BAM.
scReadSim.scATAC_GenerateBAM.ErrorBase(base, ...)	Sample random errors.
scReadSim.scATAC_GenerateBAM.ErroneousRead(...)	Generate random errors according to input real data error rates.
scReadSim.scATAC_GenerateBAM.SubstiError_Pair(...)	Generate random errors for paired-end sequencing reads according to input real data error rates.
scReadSim.scATAC_GenerateBAM.scATAC_ErrorBase(...)	Introduce random substitution errors into synthetic reads according to real data error rates.
scReadSim.scATAC_GenerateBAM.scATAC_GenerateSyntheticRead_MultiSample(...)	Multi-sample/replicate implement of scReadSim for simulating scATAC-seq synthetic reads.

scRNA_GenerateBAM

scReadSim.scRNA_GenerateBAM.flatten(x)	Flatten a nested list.
scReadSim.scRNA_GenerateBAM.cellbarcode_generator(length)	Generate random cellbarcode.
scReadSim.scRNA_GenerateBAM.scRNA_GenerateBAMCoord(...)	Generate Synthetic reads in BED format.
scReadSim.scRNA_GenerateBAM.scRNA_CombineBED(...)	Combine the bed files of foreground and background feature sets into one bed file.
scReadSim.scRNA_GenerateBAM.scRNA_BED2FASTQ(...)	Convert Synthetic reads from BED to FASTQ.
scReadSim.scRNA_GenerateBAM.AlignSyntheticBam_Single(...)	Convert Synthetic reads from FASTQ to BAM.
scReadSim.scRNA_GenerateBAM.ErrorBase(base, ...)	Sample random errors.
scReadSim.scRNA_GenerateBAM.ErroneousRead(...)	Generate random errors according to input real data error rates.
scReadSim.scRNA_GenerateBAM.SubstiError(...)	Generate random errors for single-end sequencing reads according to input real data error rates.
scReadSim.scRNA_GenerateBAM.scRNA_ErrorBase(...)	Introduce random substitution errors into synthetic reads according to real data error rates.
scReadSim.scRNA_GenerateBAM.scRNA_GenerateSyntheticRead_MultiSample(...)	Multi-sample/replicate implement of scReadSim for simulating scRNA-seq synthetic reads.

DoubletDetection

scReadSim.DoubletDetection.detectDoublet(...)

Detect doublets from real count matrix.

GenerateSyntheticCount

scReadSim.GenerateSyntheticCount.scATAC_GenerateSyntheticCount(...)	Simulate synthetic count matrix.
scReadSim.GenerateSyntheticCount.scRNA_GenerateSyntheticCount(...)	Simulate synthetic count matrix.
scReadSim.GenerateSyntheticCount.scATAC_GenerateSyntheticCount_MultiSample(...)	Multi-sample/replicate implement of scReadSim for simulating scATAC-seq synthetic count matrix.
scReadSim.GenerateSyntheticCount.scRNA_GenerateSyntheticCount_MultiSample(...)	Multi-sample/replicate implement of scReadSim for simulating scRNA-seq synthetic count matrix.

GenerateSyntheticCount_MultiOmics

scReadSim.GenerateSyntheticCount_MultiOmics.scMultiOmics_GenerateSyntheticCount(...)

Simulate synthetic multiomic count matrices.