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Overview
API
About scReadSim
Tutorials
Install required softwares of scReadSim
scReadSim for 10x scATAC-seq
scReadSim for 10x scRNA-seq
scReadSim for single-cell multiomics
scReadSim for scATAC-seq from multiple samples/conditions
scReadSim for scRNA-seq from multiple samples/conditions
scReadSim for scRNA-seq with condition effect
scReadSim for 10x scRNA-seq (exon only)
scReadSim for 10x scATAC-seq with user-designed open chromatin regions
scReadSim
Index
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Index
A
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B
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C
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D
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E
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F
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M
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S
A
AlignSyntheticBam_Pair() (in module scReadSim.scATAC_GenerateBAM)
AlignSyntheticBam_Single() (in module scReadSim.scRNA_GenerateBAM)
B
bam2MarginalCount() (in module scReadSim.Utility)
C
CallPeak() (in module scReadSim.Utility)
cellbarcode_generator() (in module scReadSim.scATAC_GenerateBAM)
(in module scReadSim.scRNA_GenerateBAM)
countmat_mainloop() (in module scReadSim.Utility)
D
detectDoublet() (in module scReadSim.DoubletDetection)
E
ErroneousRead() (in module scReadSim.scATAC_GenerateBAM)
(in module scReadSim.scRNA_GenerateBAM)
ErrorBase() (in module scReadSim.scATAC_GenerateBAM)
(in module scReadSim.scRNA_GenerateBAM)
ExtractBAMCoverage() (in module scReadSim.Utility)
F
FeatureMapping() (in module scReadSim.Utility)
find_leftnearest_nonpeak() (in module scReadSim.scATAC_GenerateBAM)
find_nearest_nonpeak() (in module scReadSim.Utility)
find_nearest_peak() (in module scReadSim.Utility)
flatten() (in module scReadSim.scATAC_GenerateBAM)
(in module scReadSim.scRNA_GenerateBAM)
M
match_nonpeak() (in module scReadSim.Utility)
match_peak() (in module scReadSim.Utility)
module
scReadSim
S
scATAC_bam2countmat_OutputPeak() (in module scReadSim.Utility)
scATAC_bam2countmat_paral() (in module scReadSim.Utility)
scATAC_bam2countmat_paral_MultiSample() (in module scReadSim.Utility)
scATAC_BED2FASTQ() (in module scReadSim.scATAC_GenerateBAM)
scATAC_CombineBED() (in module scReadSim.scATAC_GenerateBAM)
scATAC_CreateFeatureSets() (in module scReadSim.Utility)
scATAC_ErrorBase() (in module scReadSim.scATAC_GenerateBAM)
scATAC_GenerateBAMCoord() (in module scReadSim.scATAC_GenerateBAM)
scATAC_GenerateBAMCoord_OutputPeak() (in module scReadSim.scATAC_GenerateBAM)
scATAC_GenerateSyntheticCount() (in module scReadSim.GenerateSyntheticCount)
scATAC_GenerateSyntheticCount_MultiSample() (in module scReadSim.GenerateSyntheticCount)
scATAC_GenerateSyntheticRead_MultiSample() (in module scReadSim.scATAC_GenerateBAM)
scMultiOmics_GenerateSyntheticCount() (in module scReadSim.GenerateSyntheticCount_MultiOmics)
scReadSim
module
scRNA_bam2countmat_paral() (in module scReadSim.Utility)
scRNA_bam2countmat_paral_MultiSample() (in module scReadSim.Utility)
scRNA_BED2FASTQ() (in module scReadSim.scRNA_GenerateBAM)
scRNA_CombineBED() (in module scReadSim.scRNA_GenerateBAM)
scRNA_CreateFeatureSets() (in module scReadSim.Utility)
scRNA_ErrorBase() (in module scReadSim.scRNA_GenerateBAM)
scRNA_GenerateBAMCoord() (in module scReadSim.scRNA_GenerateBAM)
scRNA_GenerateSyntheticCount() (in module scReadSim.GenerateSyntheticCount)
scRNA_GenerateSyntheticCount_MultiSample() (in module scReadSim.GenerateSyntheticCount)
scRNA_GenerateSyntheticRead_MultiSample() (in module scReadSim.scRNA_GenerateBAM)
scRNA_UMIcountmat_mainloop() (in module scReadSim.Utility)
SubstiError() (in module scReadSim.scRNA_GenerateBAM)
SubstiError_Pair() (in module scReadSim.scATAC_GenerateBAM)
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