SCATEData package

Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji1

1Deparment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University

Package

SCATEData 1.4.0

Contents

1 Overview

The SCATEData is an extensive data resources containing the location of genomic regions bins, the mean and standard deviation of normalized bulk DNase-seq signals across ENCODE samples, and the clustering of the genomic bins based on bulk DNase-seq signals. These data have been formatted as GenomicRanges Bioconductor objects and hosted on Bioconductor’s ExperimentHub platform.

SCATEData provides data resources for the package SCATE to extract and enhance the sparse and discrete Single-cell ATAC-seq Signal.

For more details, see our paper describing the SCATE package:

• Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji, Single-cell ATAC-seq Signal Extraction and Enhancement with SCATE, Genome Biol 21, 161 (2020).

2 Datasets

The package contains the following datasets, which can be used by SCATE to extract and enhance the sparse Single-cell ATAC-seq signals. They are grouped into datasets useful for (i) running SCATE, and (ii) providing examples.

• Loaded by SCATE:
  • hg19.rds
  • mm10.rds
• scATAC-seq example files:
  • GSM1596831.bam
    
  • GSM1596940.bam
    
  • GSM1597041.bam
    
  • SRR1779856.bam
    
  • SRR1779973.bam
    
  • GSM1596840.bam
    
  • GSM1596942.bam
    
  • GSM1597096.bam
    
  • SRR1779874.bam
    
  • SRR1780018.bam
  • GSM1596874.bam
    
  • GSM1596944.bam
    
  • SRR1779746.bam
    
  • SRR1779956.bam
    
  • SRR1780020.bam
  • GSM1596881.bam
    
  • GSM1596961.bam
    
  • SRR1779805.bam
    
  • SRR1779959.bam
    
  • SRR1780054.bam
  • GSM1596831.bam.bai
    
  • GSM1596940.bam.bai
    
  • GSM1597041.bam.bai
    
  • SRR1779856.bam.bai
    
  • SRR1779973.bam.bai
    
  • GSM1596840.bam.bai
    
  • GSM1596942.bam.bai
    
  • GSM1597096.bam.bai
    
  • SRR1779874.bam.bai
    
  • SRR1780018.bam.bai
  • GSM1596874.bam.bai
    
  • GSM1596944.bam.bai
    
  • SRR1779746.bam.bai
    
  • SRR1779956.bam.bai
    
  • SRR1780020.bam.bai
  • GSM1596881.bam.bai
    
  • GSM1596961.bam.bai
    
  • SRR1779805.bam.bai
    
  • SRR1779959.bam.bai
    
  • SRR1780054.bam.bai

These .bam files are Single-cell ATAC-seq reads and the corresponding .bam.bai files are for indexing and searching for the reads in these files. For more extensive documentation, please refer to the metadata or help files for the objects.

3 How to load data

Please refer to SCATE tutorial for the loading and use of the data.

4 Citation

If the SCATEData package is useful in your work, please cite the following paper: - Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji, Single-cell ATAC-seq Signal Extraction and Enhancement with SCATE, Genome Biol 21, 161 (2020).