AnVIL

DOI: 10.18129/B9.bioc.AnVIL    

Bioconductor on the AnVIL compute environment

Bioconductor version: Release (3.15)

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. For the end-user, AnVIL provides fast binary package installation, utitlities for working with Terra / AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, Dockstore, and Gen3 RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.

Author: Martin Morgan [aut, cre] , Nitesh Turaga [aut], BJ Stubbs [ctb], Vincent Carey [ctb], Marcel Ramos [ctb], Sehyun Oh [ctb], Sweta Gopaulakrishnan [ctb], Valerie Obenchain [ctb]

Maintainer: Martin Morgan <mtmorgan.bioc at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AnVIL")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("AnVIL")

 

HTML	R Script	Dockstore and Bioconductor for AnVIL
HTML	R Script	Introduction to the AnVIL package
HTML	R Script	Running an AnVIL workflow within R
PDF		Reference Manual
Text		NEWS

Details

biocViews	Infrastructure, Software
Version	1.8.7
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	Artistic-2.0
Depends	R (>= 3.6), dplyr
Imports	stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), tibble, tidyselect, tidyr, rlang, BiocManager
LinkingTo
Suggests	parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me	cBioPortalData, terraTCGAdata
Imports Me	AnVILPublish
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	AnVIL_1.8.7.tar.gz
Windows Binary	AnVIL_1.8.7.zip
macOS Binary (x86_64)	AnVIL_1.8.7.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AnVIL
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AnVIL
Package Short Url	https://bioconductor.org/packages/AnVIL/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.15	Source Archive