srnadiff
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 inra.fr>
citation("srnadiff")
):
Installation
To install this package, start R (version "4.4") 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
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 | ||
NEWS | Text |
Details
biocViews | Coverage, DifferentialExpression, Epigenetics, GeneExpression, ImmunoOncology, Preprocessing, SmallRNA, Software, StatisticalMethod |
Version | 1.24.0 |
In Bioconductor since | BioC 3.7 (R-3.5) (6.5 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 |
URL |
See More
Suggests | knitr, rmarkdown, testthat, BiocManager, BiocStyle |
Linking To | Rcpp |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | srnadiff_1.24.0.tar.gz |
Windows Binary | srnadiff_1.24.0.zip |
macOS Binary (x86_64) | srnadiff_1.24.0.tgz |
macOS Binary (arm64) | srnadiff_1.24.0.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/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.19 | Source Archive |