cellbaseR
This is the released version of cellbaseR; for the devel version, see cellbaseR.
Querying annotation data from the high performance Cellbase web
Bioconductor version: Release (3.23)
This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.
Author: Mohammed OE Abdallah
Maintainer: Mohammed OE Abdallah <melsiddieg at gmail.com>
citation("cellbaseR")):
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("cellbaseR")
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("cellbaseR")| Simplifying Genomic Annotations in R | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Software, VariantAnnotation |
| Version | 1.36.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | Apache License (== 2.0) |
| Depends | R (>= 3.4) |
| Imports | methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel |
| System Requirements | |
| URL | https://github.com/melsiddieg/cellbaseR |
See More
| Suggests | BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation |
| 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 | cellbaseR_1.36.0.tar.gz |
| Windows Binary (x86_64) | cellbaseR_1.36.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | cellbaseR_1.36.0.tgz |
| macOS Binary (sonoma-arm64) | cellbaseR_1.36.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cellbaseR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cellbaseR |
| Bioc Package Browser | https://code.bioconductor.org/browse/cellbaseR/ |
| Package Short Url | https://bioconductor.org/packages/cellbaseR/ |
| Package Downloads Report | Download Stats |