snapcount
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see snapcount.
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
Bioconductor version: 3.11
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
Maintainer: Rone Charles <rcharle8 at jh.edu>
citation("snapcount")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.0.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 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), JunctionSeq, 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_1.0.0.tar.gz |
| Windows Binary | snapcount_1.0.0.zip |
| macOS 10.13 (High Sierra) | snapcount_1.0.0.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 |
| Old Source Packages for BioC 3.11 | Source Archive |