snapcount

This package is for version 3.19 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: 3.19

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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DataImport, GeneExpression, RNASeq, Sequencing, Software

Version 1.16.0

In Bioconductor since BioC 3.11 (R-4.0) (4.5 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

Suggests BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle(>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0)

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Package Archives

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

Source Package snapcount_1.16.0.tar.gz

Windows Binary (x86_64) snapcount_1.16.0.zip

macOS Binary (x86_64) snapcount_1.16.0.tgz

macOS Binary (arm64) snapcount_1.16.0.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/

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