AnVIL

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

Bioconductor on the AnVIL compute environment

Bioconductor version: Development (3.21)

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] (ORCID: ), Martin Morgan [aut] (ORCID: ), 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 sph.cuny.edu>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, Software
Version	1.19.3
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 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, BiocBaseUtils
System Requirements
URL

Suggests	parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle
Linking To
Enhances
Depends On Me	cBioPortalData
Imports Me	AnVILPublish, AnVILWorkflow, terraTCGAdata
Suggests Me	AnVILBase, AnVILGCP
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	AnVIL_1.19.3.tar.gz
Windows Binary (x86_64)	AnVIL_1.19.3.zip
macOS Binary (x86_64)	AnVIL_1.19.3.tgz
macOS Binary (arm64)	AnVIL_1.19.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AnVIL
Source Repository (Developer Access)	git clone [email protected]:packages/AnVIL
Bioc Package Browser	https://code.bioconductor.org/browse/AnVIL/
Package Short Url	https://bioconductor.org/packages/AnVIL/
Package Downloads Report	Download Stats