snapcount

DOI: 10.18129/B9.bioc.snapcount  

R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	snapcount quick start guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Coverage, DataImport, GeneExpression, RNASeq, Sequencing, Software
Version	1.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (3 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
LinkingTo
Suggests	BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle(>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0)
SystemRequirements
Enhances
URL	https://github.com/langmead-lab/snapcount
BugReports	https://github.com/langmead-lab/snapcount/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	snapcount_1.10.0.tar.gz
Windows Binary	snapcount_1.10.0.zip (64-bit only)
macOS Binary (x86_64)	snapcount_1.10.0.tgz
macOS Binary (arm64)	snapcount_1.10.0.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