⚠️ WARNING
cisTopic is deprecated, use pycisTopic instead.

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")

For installing and loading cisTopic, run:

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

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

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.

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.

cisTopic v3: Faster topic modelling based on WarpLDA (see vignettes for details).
The function runModels() is deprecated. Use runCGSModels() for modelling based on Collapsed Gibbs Sampling (equivalent to runModels()), or runWarpLDAModels() (for modelling based on WarpLDA).
Version 2 objects (with or without models) can be used and analyzed with version 3.