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.

References:

• Bingjie Zhang, Avi Srivastava, Eleni Mimitou, Tim Stuart, Ivan Raimondi, Yuhan Hao, Peter Smibert & Rahul Satija
  Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro
  Nature Biotechnology, 24 March 2022
Documentation
• scChromHMM Github page
Important Notes
• Module Name: scChromHMM (see the modules page for more information)
• Unusual environment variables set
  • SCCHROMHMM_HOME  installation directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.



[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 
 --threads 

FLAGS:
    -h, --help       Prints help information
        --onlyone    quantify only chromosome one
    -V, --version    Prints version information

OPTIONS:
    -a, --anchors ...           path to the anchors files. [Same order as fragments]
    -c, --common_cells     path to the file with cellular barcodes of common assay
    -f, --fragments ...       path to the fragment files.
    -m, --model                   path to the chromeHMM model.txt file
    -o, --output 
                path to the output directory
    -t, --threads               number of threads to use
[user@cn0861 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226