HoneyBADGER (hidden Markov model integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data) identifies and infers the presence of CNV and LOH events in single cells and reconstructs subclonal architecture using allele and expression information from single-cell RNA-sequencing data.
The overall approach is detailed in the following publication:
Fan J*, Lee HO*, Lee S, et al. Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data. Genome Res. 2018;
HoneyBADGER, we recommend using
JAGS (Just Another Gibbs Sampler) through
JAGS must be installed per your operating system requirements. Please see this R-bloggers tutorial for additional tips for installing
Additional dependencies may need to be installed from
Bioconductor such as
GenomicRanges and others:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GenomicRanges")
We welcome any bug reports, enhancement requests, and other contributions. To submit a bug report or enhancement request, please use the
HoneyBADGER GitHub issues tracker. For more substantial contributions, please fork this repo, push your changes to your fork, and submit a pull request with a good commit message.