Skip to content

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

Notifications You must be signed in to change notification settings

aertslab/cisTopic

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

⚠️ 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")

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

Version 2

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.

About

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

Resources

Stars

Watchers

Forks

Packages