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 (3.18)
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 "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | Coverage, DifferentialExpression, Epigenetics, GeneExpression, ImmunoOncology, Preprocessing, SmallRNA, Software, StatisticalMethod |
| Version | 1.21.0 |
| 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 | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | srnadiff_1.21.0.tar.gz |
| Windows Binary | srnadiff_1.21.0.zip (64-bit only) |
| macOS Binary (x86_64) | srnadiff_1.21.0.tgz |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/srnadiff/ |
| Package Short Url | https://bioconductor.org/packages/srnadiff/ |
| Package Downloads Report | Download Stats |