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Finding differentially expressed unannotated genomic regions from RNA-seq data

Bioconductor version: Release (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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

The srnadiff package HTML R Script
Reference Manual PDF


biocViews Coverage, DifferentialExpression, Epigenetics, GeneExpression, ImmunoOncology, Preprocessing, SmallRNA, Software, StatisticalMethod
Version 1.24.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends R (>= 3.6)
Imports Rcpp (>= 0.12.8), stats, methods, devtools, S4Vectors, GenomeInfoDb, rtracklayer, SummarizedExperiment, IRanges, GenomicRanges, DESeq2, edgeR, Rsamtools, GenomicFeatures, GenomicAlignments, grDevices, Gviz, BiocParallel, BiocManager, BiocStyle
System Requirements C++11
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Suggests knitr, rmarkdown, testthat, BiocManager, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package srnadiff_1.24.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) srnadiff_1.24.0.tgz
macOS Binary (arm64) srnadiff_1.24.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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