README.md

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

SCATEData

Summary

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).

Installation

The SCATEData package is freely available from Bioconductor, and can be installed by following standard Bioconductor package installation procedures:

# install BiocManager (if not already installed)
install.packages("BiocManager")

# install HDCytoData package
BiocManager::install("SCATEData")

Vignettes

Additional details are provided in the following vignettes, available from the Bioconductor website:

• SCATEData package: Overview of the package and example showing how to load the datasets
• Examples and use cases: Examples and use cases

For details on the datasets, see the manual page by typing ??SCATEData for each dataset available within the package, or the metadata from the ExperimentHub database (see "SCATEData package" vignette).

Issues

Please open an issue in this repository if you have any questions or need any assistance regarding this package.

Citation

If you find this package useful, 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).

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