Package: blit 0.2.0.9000

Yun Peng

blit: Bioinformatics Library for Integrated Tools

An all-encompassing R toolkit designed to streamline the process of calling various bioinformatics software and then performing data analysis and visualization in R. With 'blit', users can easily integrate a wide array of bioinformatics command line tools into their workflows, leveraging the power of R for sophisticated data manipulation and graphical representation.

Authors:Yun Peng [aut, cre], Shixiang Wang [aut], Jia Ding [ctb], Jennifer Lu [cph], Li Song [cph], X. Shirley Liu [cph]

blit_0.2.0.9000.tar.gz
blit_0.2.0.9000.zip(r-4.7)blit_0.2.0.9000.zip(r-4.6)blit_0.2.0.9000.zip(r-4.5)
blit_0.2.0.9000.tgz(r-4.6-any)blit_0.2.0.9000.tgz(r-4.5-any)
blit_0.2.0.9000.tar.gz(r-4.7-any)blit_0.2.0.9000.tar.gz(r-4.6-any)
blit_0.2.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
blit/json (API)
NEWS

# Install 'blit' in R:
install.packages('blit', repos = c('https://wanglabcsu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wanglabcsu/blit/issues

Pkgdown/docs site:https://wanglabcsu.github.io

On CRAN:

Conda:

bioinformaticscommand-line

6.28 score 20 stars 2 packages 6 scripts 203 downloads 48 exports 6 dependencies

Last updated from:940c2c1385. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK153
source / vignettesOK160
linux-release-x86_64OK127
macos-release-arm64OK115
macos-oldrel-arm64OK96
windows-develOK148
windows-releaseOK86
windows-oldrelOK85
wasm-releaseOK93

Exports:allele_counterappmambaappmamba_rcargarg0bcftoolsbedtoolsbowtie2bwacellrangercmd_backgroundcmd_condacmd_condaenvcmd_envpathcmd_envvarcmd_helpcmd_on_exitcmd_on_failcmd_on_startcmd_on_succeedcmd_parallelcmd_runcmd_wdCommandcondaexecfastpfastq_pairfastq_read_pairfreebayesgistic2install_appmambakraken_toolskraken2make_commandminimap2perlpyscenicpythonsamtoolsseqkitsnpEffstrelkatrust4trust4_gene_namestrust4_imgt_annotuninstall_appmambavarscan

Dependencies:clilifecycleprocessxpsR6rlang

Readme and manuals

Help Manual

Help pageTopics
Run alleleCountallele_counter
Manage Environment with 'micromamba'appmamba appmamba_rc install_appmamba uninstall_appmamba
Deliver arguments of commandarg arg0
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.bcftools
Run bedtoolsbedtools
Run bowtie2bowtie2
Run BWAbwa
Run cellrangercellranger
Set 'conda-like' environment prefix to the 'PATH' environment variablescmd_conda
Schedule expressions to runcmd_on_exit cmd_on_fail cmd_on_start cmd_on_succeed
Execute a list of commandscmd_parallel
Execute commandcmd_background cmd_help cmd_run
Setup the context for the commandcmd_condaenv cmd_envpath cmd_envvar cmd_wd
R6 Class to prepare command parameters.Command
Run condaconda
Invoke a System Commandexec
Run fastpfastp
FASTQ PAIRfastq_pair fastq_read_pair
Run freebayesfreebayes
Run GISTIC2gistic2
KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs.kraken_tools
Running Kraken2kraken2
Helper function to create new command.make_command
Run minimap2minimap2
Perl is a highly capable, feature-rich programming language with over 36 years of development.perl
Run pyscenicpyscenic
Python is a programming language that lets you work quickly and integrate systems more effectively.python
Python is a programming language that lets you work quickly and integrate systems more effectively.samtools
Run seqkitseqkit
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).snpEff
Run strelkastrelka
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq datatrust4 trust4_gene_names trust4_imgt_annot
VarScan is a platform-independent software tool developed at the Genome Institute at Washington University to detect variants in NGS data.varscan