Package Recipe 'bioconductor-srnadiff'

recipe bioconductor-srnadiff

Finding differentially expressed unannotated genomic regions from RNA-seq data

Homepage: https://bioconductor.org/packages/3.12/bioc/html/srnadiff.html
License: GPL-3
Recipe: /bioconductor-srnadiff/meta.yaml

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.

package bioconductor-srnadiff¶

Versions

1.10.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.2.0-0

Depends

bioconductor-biocparallel >=1.24.0,<1.25.0
bioconductor-biocstyle >=2.18.0,<2.19.0
bioconductor-deseq2 >=1.30.0,<1.31.0
bioconductor-genomeinfodb >=1.26.0,<1.27.0
bioconductor-genomicalignments >=1.26.0,<1.27.0
bioconductor-genomicfeatures >=1.42.0,<1.43.0
bioconductor-genomicranges >=1.42.0,<1.43.0
bioconductor-gviz >=1.34.0,<1.35.0
bioconductor-iranges >=2.24.0,<2.25.0
bioconductor-rsamtools >=2.6.0,<2.7.0
bioconductor-rtracklayer >=1.50.0,<1.51.0
bioconductor-s4vectors >=0.28.0,<0.29.0
bioconductor-summarizedexperiment >=1.20.0,<1.21.0
libblas >=3.8.0,<4.0a0
libgcc-ng >=7.5.0
liblapack >=3.8.0,<4.0a0
libstdcxx-ng >=7.5.0
r-base >=4.0,<4.1.0a0
r-biocmanager
r-devtools
r-rcpp >=0.12.8

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-srnadiff

and update with:

conda update bioconductor-srnadiff

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-srnadiff:<tag>

(see bioconductor-srnadiff/tags for valid values for <tag>)

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-srnadiff/README.html)