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srnadiff

This is the development version of srnadiff; for the stable release version, see srnadiff.

Finding differentially expressed unannotated genomic regions from RNA-seq data


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("srnadiff")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
The srnadiff package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DifferentialExpression, Epigenetics, GeneExpression, ImmunoOncology, Preprocessing, SmallRNA, Software, StatisticalMethod
Version 1.23.1
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends R (>= 3.6)
Imports Rcpp (>= 0.12.8), methods, devtools, S4Vectors, GenomeInfoDb, rtracklayer, SummarizedExperiment, IRanges, GenomicRanges, DESeq2, edgeR, Rsamtools, GenomicFeatures, GenomicAlignments, grDevices, Gviz, BiocParallel, BiocStyle, BiocManager
System Requirements C++11
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Suggests knitr, rmarkdown, testthat, BiocManager, BiocStyle
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Package Archives

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

Source Package srnadiff_1.23.1.tar.gz
Windows Binary srnadiff_1.23.1.zip
macOS Binary (x86_64) srnadiff_1.23.1.tgz
macOS Binary (arm64) srnadiff_1.23.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/srnadiff
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/srnadiff
Bioc Package Browser https://code.bioconductor.org/browse/srnadiff/
Package Short Url https://bioconductor.org/packages/srnadiff/
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