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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

Version 3

• 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.

Version 2

• 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.

News

2019-12-20:

• 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.