nbahti/cistopic

cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

News

• 2019-7-3:
  • Liftover vignettes for mm10 and hg38 genome assemblies.

cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

cisTopic is an R-package to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

Dependencies (for R < 3.5)

The following packages have to be installed manually before installing cisTopic:

devtools::install_github("aertslab/RcisTarget")
devtools::install_github("aertslab/AUCell")

Installation

For installing and loading cisTopic, run:

devtools::install_github("aertslab/cisTopic")
library(cisTopic)

Databases

RcisTarget feather databases are available at https://resources.aertslab.org/cistarget/.

Tutorials

• Basic tutorial on simulated single cell epigenomes from melanoma cell lines. Data available here.
• 10X tutorial on the 5k PBMC data set from 10X. Data available here.
• Running GREAT and motif enrichment with the mm10 and hg38 genome assemblies.