Tool: ChromSCape - A R/Shiny application to analyze single-cell epigenomics data
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5 months ago
pacome.pr ▴ 100

Hello everyone,

I would like to present ChromSCape, a Bioconductor R package and Shiny application for both biologists and bioinformaticians to analyze single-cell epigenomic datasets (scChIP-seq, scATAC-seq, scCUT&TAG ... ) in an user friendly and interactive way.

To install the package, make sure you have R4.0 and Bioconductor 3.12

 if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("ChromSCape")

To start, just load the package and launch the app :

launchApp()

-> If you want more details on the hows and whats of the app, check the vignette

-> If you don't have data yet, here are some publicly available single-cell epigenomic datasets you can directly input in ChromSCape

-> If you are interested about how it compares to other tools on scATAC-seq and it's use on scChIP-seq, scCUT&TAG and scChIL-seq, please read the article (open acess).

-> If you have issues / bugs / ideas for improvements, please check the GitHub

-> If you are just curious, check the look & feel with a small demo

Cheers,
PacĂ´me

ChIP-Seq scChIP-seq scATAC-seq single-cell R Tool • 289 views
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