snapcount
This is thereleased version of snapcount; for the devel version, seesnapcount.
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | 1.22.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 years) |
| License | MIT + fileLICENSE |
| 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | snapcount_1.22.0.tar.gz |
| Windows Binary (x86_64) | snapcount_1.22.0.zip |
| macOS Binary (x86_64) | snapcount_1.22.0.tgz |
| macOS Binary (arm64) | snapcount_1.22.0.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 |