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SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement

Introductions

Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscape in single cells. Due to data sparsity and discreteness, analyzing scATAC-seq data is challenging. Existing computational methods cannot accurately reconstruct activities of individual cis-regulatory elements (CREs) in individual cells. We present a new statistical framework, SCATE, that adaptively integrates information from co-activated CREs, similar cells, and publicly available regulome data to substantially increase the accuracy for estimating individual CRE activities in single cell and rare cell subpopulations.

SCATE Installation

SCATE software can be installed via Github. Users should have R installed on their computer before installing SCATE. R version needs to be at least 3.5.x or higher. R can be downloaded here: http://www.r-project.org/.

For Windows users, Rtools is also required to be installed. Rtools can be downloaded here: (https://cloud.r-project.org/bin/windows/Rtools/). For R version 3.5.x, Rtools35.exe is recommended. Use default settings to perform the installation.

For mac users, if there is any problem with installation problem, please try download and install clang-8.0.0.pkg from the following URL: https://cloud.r-project.org/bin/macosx/tools/clang-8.0.0.pkg

To install the latest version of SCATE package via Github, run following commands in R:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("GenomicAlignments","preprocessCore"))
if (!require("devtools"))
  install.packages("devtools")
devtools::install_github("zji90/SCATE")

If there is any problem with the installation process, please make sure you have R version at least 3.5.x and you have installed Rtools (Windows users) or clang (mac users). If the problem still occurs, please contact the author (see below)

User Manual

Check the following page for PDF version of the user manual: https://github.com/zji90/SCATE/raw/master/inst/doc/SCATE.pdf

Check below link for the R code of the user manual.

https://github.com/zji90/SCATE/blob/master/inst/doc/SCATE.R

Contact the Author

Author: Zhicheng Ji, Hongkai Ji

Report bugs and provide suggestions by sending email to:

Maintainer: Zhicheng Ji (zji4@jhu.edu)

Or open a new issue on this Github page

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SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement

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