AnVILPublish
This is the development version of AnVILPublish; for the stable release version, see AnVILPublish.
Publish Packages and Other Resources to AnVIL Workspaces
Bioconductor version: Development (3.24)
Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the 'DASHBOARD'. Vignettes are translated to python notebooks ready for evaluation in AnVIL.
Author: Marcel Ramos [aut, cre]
, Martin Morgan [aut]
, Kayla Interdonato [aut], Vincent Carey [ctb]
, NHGRI [fnd] (GrantNo.: U24HG010263)
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("AnVILPublish")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("AnVILPublish")
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("AnVILPublish")| Publishing R / Bioconductor packages to AnVIL Workspaces | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, Software |
| Version | 1.23.5 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | Artistic-2.0 |
| Depends | |
| Imports | AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats |
| System Requirements | Quarto command line tool ( |
| URL | https://github.com/Bioconductor/AnVILPublish/ |
| Bug Reports | https://github.com/Bioconductor/AnVILPublish/issues |
See More
| Suggests | AnVILBase, knitr, BiocStyle, GCPtools, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | BiocAzul |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | AnVILPublish_1.23.5.tar.gz |
| Windows Binary (x86_64) | AnVILPublish_1.23.5.zip |
| macOS Binary (big-sur-x86_64) | AnVILPublish_1.23.5.tgz |
| macOS Binary (sonoma-arm64) | AnVILPublish_1.23.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/AnVILPublish |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AnVILPublish |
| Bioc Package Browser | https://code.bioconductor.org/browse/AnVILPublish/ |
| Package Short Url | https://bioconductor.org/packages/AnVILPublish/ |
| Package Downloads Report | Download Stats |