AnVILWorkflow
This is the released version of AnVILWorkflow; for the devel version, see AnVILWorkflow.
Run workflows implemented in Terra/AnVIL workspace
Bioconductor version: Release (3.23)
The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The main cloud-based genomics platform deported by the AnVIL project is Terra. The AnVILWorkflow package allows remote access to Terra implemented workflows, enabling end-user to utilize Terra/ AnVIL provided resources - such as data, workflows, and flexible/scalble computing resources - through the conventional R functions.
Author: Sehyun Oh [aut, cre]
, Marcel Ramos [ctb]
, Kai Gravel-Pucillo [aut]
Maintainer: Sehyun Oh <shbrief at gmail.com>
citation("AnVILWorkflow")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("AnVILWorkflow")
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("AnVILWorkflow")| Quickstart - RNAseq analysis using salmon | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0), AnVILGCP, AnVILBase, httr |
| Imports | AnVIL, dplyr, jsonlite, rlang, tibble, tidyr, utils, methods, plyr, stringr |
| System Requirements | |
| URL | https://github.com/shbrief/AnVILWorkflow |
| Bug Reports | https://github.com/shbrief/AnVILWorkflow/issues |
See More
| Suggests | knitr, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | AnVILWorkflow_1.11.0.tar.gz |
| Windows Binary (x86_64) | AnVILWorkflow_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/AnVILWorkflow |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AnVILWorkflow |
| Bioc Package Browser | https://code.bioconductor.org/browse/AnVILWorkflow/ |
| Package Short Url | https://bioconductor.org/packages/AnVILWorkflow/ |
| Package Downloads Report | Download Stats |