Run pyscenic

Run pyscenic

Usage

pyscenic(subcmd = NULL, ..., pyscenic = NULL)

Arguments

subcmd

Sub-Command of pyscenic.

...

<dynamic dots> Additional arguments passed to pyscenic subcmd command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote(). Details see: cmd_help(pyscenic subcmd()).

pyscenic

A string of path to pyscenic command.

Value

A command object.

See also

• https://github.com/aertslab/pySCENIC

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_condaenv()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

Other commands: allele_counter(), bcftools(), bedtools(), bowtie2(), bwa(), cellranger(), conda(), fastp(), fastq_pair(), gistic2(), kraken2(), kraken_tools(), perl(), python(), samtools(), seqkit(), snpEff(), trust4(), varscan()