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README.md

SCRAT: Single-Cell Regulome Analysis Tool

SCRAT Online User Interface

SCRAT is also available online at https://zhiji.shinyapps.io/scrat/

SCRAT Installation

SCRAT software can be installed via Github. Users should have R installed on their computer before installing SCRAT. R can be downloaded here: http://www.r-project.org/ (64-bit R is recommended). Users should first install the SCRAT data packages by running following commands in R:

if (!require("devtools"))
  install.packages("devtools")
devtools::install_github("zji90/SCRATdatahg19")
devtools::install_github("zji90/SCRATdatahg38")
devtools::install_github("zji90/SCRATdatamm10")
devtools::install_github("zji90/SCRATdatamm9")

To install the latest version of SCRAT package via Github, run following commands in R (R version 3.2.5 and up is recommended. See Q & A if you want to install SCRAT on an older version of R):

source("https://raw.githubusercontent.com/zji90/SCRATdata/master/installcode.R")

To launch user interface after installation, run following commands in R:

library(SCRAT)
SCRATui()

SCRAT User Manual

SCRAT user manual is available on Github: https://github.com/zji90/SCRATdata/blob/master/manual.pdf

SCRAT Example Data

SCRAT example data from GM12878 and HEK293T single-cell ATAC-seq are available on Github: https://github.com/zji90/SCRATdata

SCRAT example data can also be directly loaded in SCRAT UI after the SCRAT example data package is installed. To install the SCRAT example data package, please use the following command:

if (!require("devtools"))
  install.packages("devtools")
devtools::install_github("zji90/SCRATexample")

Citation

Please cite the following paper: Ji Z, Zhou W, Ji H. Single-cell regulome data analysis by SCRAT. Bioinformatics. 2017 Sep 15;33(18):2930-2932.

Q & A

How to install SCRAT with older versions of R (e.g., R 3.1.3)

Since older version of R does not support https connection, to install the SCRAT package, instead of using:

source("https://raw.githubusercontent.com/zji90/SCRATdata/master/installcode.R")

Please use the following commands:

source("http://bioconductor.org/biocLite.R")
biocLite("GenomicAlignments")
if(!require("shiny")) install.packages("shiny",dependencies=T)
if(!require("ggplot2")) install.packages("ggplot2",dependencies=T)
if(!require("reshape2")) install.packages("reshape2",dependencies=T)
if(!require("gplots")) install.packages("gplots",dependencies=T)
if(!require("pheatmap")) install.packages("pheatmap",dependencies=T)
if(!require("scatterD3")) install.packages("scatterD3",dependencies=T)
if(!require("DT")) install.packages("DT",dependencies=T)
if(!require("mclust")) install.packages("mclust",dependencies=T)
if(!require("tsne")) install.packages("tsne",dependencies=T)
if(!require("devtools")) install.packages("devtools",dependencies=T)
if(!require("png")) install.packages("png",dependencies=T)
devtools::install_github("zji90/SCRAT")

Contact the Author

Author: Zhicheng Ji, Weiqiang Zhou, 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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