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AnVIL

This is the development version of AnVIL; for the stable release version, see AnVIL.

Bioconductor on the AnVIL compute environment


Bioconductor version: Development (3.20)

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

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.17.9
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License Artistic-2.0
Depends R (>= 3.6), dplyr, AnVILBase
Imports stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), yaml, tibble, tidyselect, tidyr, rlang, shiny, DT, miniUI, htmltools, BiocManager, BiocBaseUtils
System Requirements
URL
See More
Suggests parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle
Linking To
Enhances
Depends On Me cBioPortalData, terraTCGAdata
Imports Me AnVILPublish, AnVILWorkflow
Suggests Me AnVILBase
Links To Me
Build Report Build Report

Package Archives

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

Source Package AnVIL_1.17.9.tar.gz
Windows Binary AnVIL_1.17.9.zip
macOS Binary (x86_64) AnVIL_1.17.9.tgz
macOS Binary (arm64) AnVIL_1.17.9.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