DOI: 10.18129/B9.bioc.srnadiff  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see srnadiff.

Finding differentially expressed unannotated genomic regions from RNA-seq data

Bioconductor version: 3.16

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>

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biocViews Coverage, DifferentialExpression, Epigenetics, GeneExpression, ImmunoOncology, Preprocessing, SmallRNA, Software, StatisticalMethod
Version 1.18.2
In Bioconductor since BioC 3.7 (R-3.5) (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
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SystemRequirements C++11
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