- 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.
cisTopic is an R-package to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
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.
- Running GREAT and motif enrichment with the mm10 and hg38 genome assemblies.
- 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.