snapcount
This is the development version of snapcount; for the stable release version, see snapcount.
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
Bioconductor version: Development (3.24)
snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various summarized measures of expression across one or more regions/genes per-sample (e.g. percent spliced in).
Author: Rone Charles [aut, cre]
Maintainer: Rone Charles <rcharle8 at jh.edu>
citation("snapcount")):
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("snapcount")
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("snapcount")| snapcount quick start guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, DataImport, GeneExpression, RNASeq, Sequencing, Software |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0.0) |
| Imports | R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/langmead-lab/snapcount |
| Bug Reports | https://github.com/langmead-lab/snapcount/issues |
See More
| Suggests | BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle(>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) |
| 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 | snapcount_1.25.0.tar.gz |
| Windows Binary (x86_64) | snapcount_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | snapcount_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | snapcount_1.25.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/snapcount |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/snapcount |
| Bioc Package Browser | https://code.bioconductor.org/browse/snapcount/ |
| Package Short Url | https://bioconductor.org/packages/snapcount/ |
| Package Downloads Report | Download Stats |