search

ytomofuji / scLinaX

This is a repository of the scLinaX R package developed in the Tomofuji et al (Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues).
https://ytomofuji.github.io/scLinaX/
Other
5 stars 1 forks source link

readme

scLinaX

scLinaX is software for the quantification of the escape from X chromosome inactivation (XCI). Input of the scLinaX is a single-cell level allele-specific expression profile generated from single-cell RNA-seq (scRNA-seq) data (germline genotype data is optional).

Overview of scLinaX

Overview of scLinaX

scLinaX also has an extension to the multi-modal single-cell omics data, scLinaX-multi. scLinaX-multi can evaluate the escape from XCI at the chromatin accessibility level. scLinaX-multi takes allele-specific read count data for both of the RNA and ATAC data.

Overview of scLinaX-multi

Overview of scLinaX-multi

Installation

You can install the development version of scLinaX from GitHub with:

# install.packages("devtools")
devtools::install_github("ytomofuji/scLinaX")

User Guide

Please see scLinaX User Guide.

Contact

Yoshihiko Tomofuji: ytomofuji_at_sg.med.osaka-u.ac.jp