SCATEData-package: Data package for SCATE to extract and enhance the sparse and...

In Winnie09/SCATEData: Data for SCATE (Single-cell ATAC-seq Signal Extraction and Enhancement)

Description

Data package for SCATE which is a software for extracting and enhancing the sparse and discrete Single-cell ATAC-seq Signal. This package contains data in the GenomicRanges format that SCATE needs for compiling examples or running the algorithm. It is hosted on Bioconductor ExperimentHub.

Details

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.

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.

How to load data

Please refer to ['SCATE' tutorial](https://github.com/Winnie09/SCATE) for the loading and use of the data.

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*](https://doi.org/10.1186/s13059-020-02075-3), Genome Biol 21, 161 (2020).

Winnie09/SCATEData documentation built on Oct. 8, 2020, 3:43 p.m.