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srnadiff

Finding differentially expressed unannotated genomic regions from RNA-seq data

Bioconductor version: Release (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>

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

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

Reference Manual PDF

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
Linking To Rcpp
Suggests knitr, rmarkdown, testthat, BiocManager, BiocStyle
System Requirements C++11
Enhances
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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/
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