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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 (3.19)

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 (from within R, enter citation("snapcount")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 PDF
NEWS Text
LICENSE Text

Details

biocViews Coverage, DataImport, GeneExpression, RNASeq, Sequencing, Software
Version 1.15.0
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), devtools, BiocStyle(>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

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

Source Package snapcount_1.15.0.tar.gz
Windows Binary snapcount_1.15.0.zip
macOS Binary (x86_64) snapcount_1.15.0.tgz
macOS Binary (arm64) snapcount_1.15.0.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