srnadiff

DOI: 10.18129/B9.bioc.srnadiff    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see srnadiff.

Finding differentially expressed unannotated genomic regions from RNA-seq data

Bioconductor version: 3.15

srnadiff is a package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation. To do so, the package implements the identify-then-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.

Author: Zytnicki Matthias [aut, cre], Gonzalez Ignacio [aut]

Maintainer: Zytnicki Matthias <matthias.zytnicki at inra.fr>

Installation

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

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

BiocManager::install("srnadiff")

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("srnadiff")

 

HTML	R Script	The srnadiff package
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DifferentialExpression, Epigenetics, GeneExpression, ImmunoOncology, Preprocessing, SmallRNA, Software, StatisticalMethod
Version	1.16.0
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	Rcpp (>= 0.12.8), methods, devtools, S4Vectors, GenomeInfoDb, rtracklayer, SummarizedExperiment, IRanges, GenomicRanges, DESeq2, edgeR, baySeq, Rsamtools, GenomicFeatures, GenomicAlignments, grDevices, Gviz, BiocParallel, BiocStyle, BiocManager
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, testthat, BiocManager, BiocStyle
SystemRequirements	C++11
Enhances
URL
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	srnadiff_1.16.0.tar.gz
Windows Binary	srnadiff_1.16.0.zip (64-bit only)
macOS Binary (x86_64)	srnadiff_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/srnadiff
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/srnadiff
Package Short Url	https://bioconductor.org/packages/srnadiff/
Package Downloads Report	Download Stats