Package: RcwlPipelines 1.29.0

Qiang Hu

RcwlPipelines: Bioinformatics pipelines based on Rcwl

A collection of Bioinformatics tools and pipelines based on R and the Common Workflow Language.

Authors:Qiang Hu [aut, cre], Qian Liu [aut], Shuang Gao [aut]

RcwlPipelines_1.29.0.tar.gz
RcwlPipelines_1.29.0.zip(r-4.7)RcwlPipelines_1.29.0.zip(r-4.6)RcwlPipelines_1.29.0.zip(r-4.5)
RcwlPipelines_1.29.0.tgz(r-4.6-any)RcwlPipelines_1.29.0.tgz(r-4.5-any)
RcwlPipelines_1.29.0.tar.gz(r-4.7-any)RcwlPipelines_1.29.0.tar.gz(r-4.6-any)
RcwlPipelines_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RcwlPipelines/json (API)

# Install 'RcwlPipelines' in R:

install.packages('RcwlPipelines', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:RcwlPipelines-1.29.0(bioc 3.24)RcwlPipelines-1.28.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software workflowstep alignment preprocessing qualitycontrol dnaseq rnaseq dataimport immunooncology

5.18 score 1 packages 34 scripts 12 exports 112 dependencies

Last updated from:37a9fdc7ee. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	181
linux-devel-x86_64	NOTE	340
source / vignettes	OK	241
linux-release-x86_64	NOTE	328
macos-release-arm64	NOTE	124
macos-oldrel-arm64	NOTE	115
windows-devel	NOTE	172
windows-release	NOTE	165
windows-oldrel	NOTE	170
wasm-release	OK	195

Exports:Command Container cwlHub cwlInstall cwlLoad cwlSearch cwlUpdate mcols searchContainer show title Type

Dependencies:askpass backports base64enc base64url basilisk batchtools BH BiocFileCache BiocGenerics BiocParallel bit bit64 blob brew bslib cachem checkmate cli clipr codetools commonmark cpp11 crayon curl data.table DBI dbplyr DiagrammeR digest dir.expiry dplyr evaluate farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics git2r glue here highr hms htmltools htmlwidgets httpuv httr httr2 igraph jquerylib jsonlite knitr labeling lambda.r later lattice lifecycle magrittr Matrix memoise mime openssl otel pillar pkgconfig png prettyunits progress promises purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppTOML Rcwl readr reticulate rlang rmarkdown rprojroot RSQLite rstudioapi S4Vectors sass scales shiny snow sourcetools stringi stringr sys tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite visNetwork vroom withr xfun xtable yaml

RcwlPipelines: Bioinformatics tools and pipelines based on Rcwl

Installation | Project resources | The R recipes and cwl scripts | Tutorial book | RcwlPipelines core functions | cwlUpdate | cwlSearch | cwlLoad | Customize a tool or pipeline | Run a tool or pipeline | SessionInfo

Rendered fromRcwlPipelines.Rmdusingknitr::rmarkdown

Last update: 2021-02-25
Started: 2019-03-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
cwlHub	Command Container cwlHub cwlHub-class mcols,cwlHub-method show,cwlHub-method title Type [,cwlHub,ANY,ANY,ANY-method
cwlInstall	cwlInstall
cwlLoad	cwlLoad
cwlSearch	cwlSearch
cwlUpdate	cwlUpdate
RcwlPipelines	RcwlPipelines
seawrch containers	searchContainer

Usage by other packages (reverse dependencies)