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Bioconductor - snapcount

snapcount

This is the released version of snapcount; for the devel version, see snapcount.

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

Bioconductor version: Release (3.21)

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 "4.5") 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")
Details biocViews Coverage, DataImport, GeneExpression, RNASeq, Sequencing, Software Version 1.20.0 In Bioconductor since BioC 3.11 (R-4.0) (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 Package Archives

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

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