scChromHMM provides a suite of tools for rapid processing of single-cell histone modification data to perform chromatin states analysis of the genome within each single-cell. It is an extention of bulk ChromHMM framework, which consumes the HMM model learned from ChromHMM and perform chromatin state analysis by running forward-backward algorithm for each single-cell.
[user@biowulf]$ sinteractive [user@cn0861 ~]$ module scChromHMM [+] Loading singularity 3.8.5-1 on cn4177 [+] Loading scChromHMM 20220610 ...
[user@cn0861 ~]$ schrom -h chrom 0.1.0 Avi Srivastava, Bingjie Zhang, Rahul Satija Generate summary stats for multimodal data. USAGE: schrom [SUBCOMMAND] FLAGS: -h, --help Prints help information -V, --version Prints version information SUBCOMMANDS: help Prints this message or the help of the given subcommand(s) hmm A subcommand to run hmm. transform A subcommand to transform long form matrices to short. [user@cn0861 ~]$ schrom hmm -h schrom-hmm A subcommand to run hmm. USAGE: schrom hmm [FLAGS] --anchors... --common_cells --fragments ... --model --output