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AnVIL

Bioconductor on the AnVIL compute environment

Bioconductor version: Release (3.17)

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, and Dockstore RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.

Author: Martin Morgan [aut, cre] , Kayla Interdonato [aut], 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>

Citation (from within R, enter citation("AnVIL")):

Installation

To install this package, start R (version "4.3") 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")
Dockstore and Bioconductor for AnVIL HTML R Script
Introduction to the AnVIL package HTML R Script
Running an AnVIL workflow within R HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Infrastructure, Software
Version 1.12.3
In Bioconductor since BioC 3.11 (R-4.0) (3.5 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, shiny, DT, miniUI, htmltools, BiocManager
Linking To
Suggests parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools
System Requirements
Enhances
URL
See More
Depends On Me cBioPortalData, terraTCGAdata
Imports Me AnVILPublish, AnVILWorkflow
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package AnVIL_1.12.3.tar.gz
Windows Binary AnVIL_1.12.3.zip
macOS Binary (x86_64) AnVIL_1.12.3.tgz
macOS Binary (arm64) AnVIL_1.12.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/AnVIL
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/AnVIL
Bioc Package Browser https://code.bioconductor.org/browse/AnVIL/
Package Short Url https://bioconductor.org/packages/AnVIL/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive