demo.sp

Data from single nucleus ATAC-seq experiment on secondary motor cortex
in adult mouse brain. The data is down-sampled to 171 cells with 27,348 100kb bins,
999 peaks and 1,000 genes.

datasets

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.

Rongxin Fang

SnapATAC

Single Nucleus Analysis Package for ATAC-Seq

demo.sp function

An object of class <code>"snap"</code> with 100 cells:<dl class="dl-horizontal">
 <dt>metData</dt><dd>meta data of each cell</dd>
 <dt>bmat</dt><dd>cell x bin matrix</dd>
 <dt>pmat</dt><dd>cell x peak matrix</dd>
 <dt>gmat</dt><dd>cell x gene matrix</dd>
 <dt>jmat</dt><dd>jaccard index matrix object</dd>
 <dt>graph</dt><dd>knn graph</dd>
 <dt>cluster</dt><dd>cluster result</dd>
 <dt>tsne</dt><dd>tsne cooridnates</dd>
 <dt>umap</dt><dd>umap cooridnates</dd>
</dl>

Format

Single Nucleus ATAC-seq Object — demo.sp

An object of class <code>"snap"</code> with 100 cells:<dl class='dl-horizontal'>
 <dt>metData</dt><dd>meta data of each cell</dd>
 <dt>bmat</dt><dd>cell x bin matrix</dd>
 <dt>pmat</dt><dd>cell x peak matrix</dd>
 <dt>gmat</dt><dd>cell x gene matrix</dd>
 <dt>jmat</dt><dd>jaccard index matrix object</dd>
 <dt>graph</dt><dd>knn graph</dd>
 <dt>cluster</dt><dd>cluster result</dd>
 <dt>tsne</dt><dd>tsne cooridnates</dd>
 <dt>umap</dt><dd>umap cooridnates</dd>
</dl>

demo.sp: Single Nucleus ATAC-seq Object

Description

Usage

Arguments

Format

Examples