predictGenePeakPair

input.mat

Name of the target gene. It must be a gene in the cell-by-gene matrix [NULL].

gene.name

A genomic range object that contains the flanking window of the target gene [NULL].

gene.loci

A logical variable indicates if to run this in parallel using multiple processors [FALSE].

do.par

A numeric class that indicates the number of cores to use for calculation [1].

num.cores

Link Distal Regulatory Elements (peaks) to Putative Target Genes

A fast and accurate analysis toolkit for single cell ATAC-seq. Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and reveal cell-type specific regulatory landscapes. However, the exceeding data sparsity has posed unique challenges for the data analysis. SnapATAC is an end-to-end bioinformatics pipeline for analyzing large-scale single cell ATAC-seq data which includes quality control, normalization, clustering analysis, differential analysis, motif inference and exploration of single cell ATAC-seq sequencing data. See Preissl S, Fang R, et al (2018) <doi:10.1038/s41593-018-0079-3> for more details.

predictGenePeakPair: Link Distal Regulatory Elements (peaks) to Putative Target Genes

Description

Usage

Arguments

Value