sevenbridges
This is the released version of sevenbridges; for the devel version, see sevenbridges.
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
Bioconductor version: Release (3.23)
R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.
Author: Phil Webster [aut, cre], Soner Koc [aut]
, Nan Xiao [aut], Tengfei Yin [aut], Dusan Randjelovic [ctb], Emile Young [ctb], Velsera [cph, fnd]
Maintainer: Phil Webster <phil.webster at velsera.com>
citation("sevenbridges")):
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("sevenbridges")
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("sevenbridges")| Complete Guide for Seven Bridges API R Client | HTML | R Script |
| Creating Your Docker Container and Command Line Interface (with docopt) | HTML | R Script |
| Describe and Execute CWL Tools/Workflows in R | HTML | R Script |
| Find Data on CGC via Data Browser and Datasets API | HTML | R Script |
| IDE Container: RStudio Server, Shiny Server, and More | HTML | R Script |
| Master Tutorial: Use R for Cancer Genomics Cloud | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, Software, ThirdPartyClient |
| Version | 1.42.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | Apache License 2.0 | file LICENSE |
| Depends | methods, utils, stats |
| Imports | httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, data.table |
| System Requirements | |
| URL | https://www.sevenbridges.com https://sbg.github.io/sevenbridges-r/ https://github.com/sbg/sevenbridges-r |
| Bug Reports | https://github.com/sbg/sevenbridges-r/issues |
See More
| Suggests | knitr, rmarkdown, testthat, readr |
| 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 | sevenbridges_1.42.0.tar.gz |
| Windows Binary (x86_64) | sevenbridges_1.42.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | sevenbridges_1.42.0.tgz |
| macOS Binary (sonoma-arm64) | sevenbridges_1.42.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sevenbridges |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sevenbridges |
| Bioc Package Browser | https://code.bioconductor.org/browse/sevenbridges/ |
| Package Short Url | https://bioconductor.org/packages/sevenbridges/ |
| Package Downloads Report | Download Stats |