Package index • blit

R6 class

Core R6 class for encapsulating command parameters and building command objects.

Command: R6 Class to prepare command parameters.

Execute command

Functions for executing commands, including foreground, background, and parallel execution.

exec(): Invoke a System Command

cmd_run() cmd_help() cmd_background(): Execute command

cmd_parallel(): Execute a list of commands

Environment context

Set up the execution context, such as working directory, environment variables, and dependency management.

cmd_wd() cmd_envvar() cmd_envpath() cmd_condaenv(): Setup the context for the command

conda(): Run conda

appmamba() install_appmamba() uninstall_appmamba() appmamba_rc(): Manage Environment with micromamba

cmd_conda() deprecated: Set conda-like environment prefix to the PATH environment variables

Schedule expressions

Define hooks to run before, after, or on success/failure of a command.

cmd_on_start() cmd_on_exit() cmd_on_fail() cmd_on_succeed(): Schedule expressions to run

Genomic tools

Wrappers for common genomic data processing and analysis tools.

allele_counter(): Run alleleCount

bcftools(): BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

bedtools(): Run bedtools

bowtie2(): Run bowtie2

bwa(): Run BWA

samtools(): Python is a programming language that lets you work quickly and integrate systems more effectively.

seqkit(): Run seqkit

varscan(): VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.

snpEff(): Genetic variant annotation, and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).

gistic2(): Run GISTIC2

Transcriptomic tools

Wrappers for transcriptome sequencing data processing and analysis tools.

cellranger(): Run cellranger

fastp(): Run fastp

fastq_pair() fastq_read_pair(): FASTQ PAIR

kraken2(): Running Kraken2

kraken_tools(): KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs.

trust4() trust4_imgt_annot() trust4_gene_names(): TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data

pyscenic(): Run pyscenic

Development

Developer utilities for extending functionality and creating new command interfaces.

make_command(): Helper function to create new command.

arg() arg0(): Deliver arguments of command

Scripting interfaces

Interfaces to external scripting languages for seamless integration with existing scripts.

python(): Python is a programming language that lets you work quickly and integrate systems more effectively.

perl(): Perl is a highly capable, feature-rich programming language with over 36 years of development.