srnadiff

DOI: 10.18129/B9.bioc.srnadiff  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see srnadiff.

Finding differentially expressed unannotated genomic regions from RNA-seq data

Bioconductor version: 3.17

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 "4.3") 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

PDF		Reference Manual

Details

biocViews	Coverage, DifferentialExpression, Epigenetics, GeneExpression, ImmunoOncology, Preprocessing, SmallRNA, Software, StatisticalMethod
Version	1.20.0
In Bioconductor since	BioC 3.7 (R-3.5) (5.5 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
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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