recipe bioconductor-srnadiff

Finding differentially expressed unannotated genomic regions from RNA-seq data

Homepage

https://bioconductor.org/packages/3.10/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

1.6.0-0, 1.4.0-1, 1.2.0-0

Depends

• bioconductor-biocparallel >=1.20.0,<1.21.0

• bioconductor-biocstyle >=2.14.0,<2.15.0

• bioconductor-deseq2 >=1.26.0,<1.27.0

• bioconductor-genomeinfodb >=1.22.0,<1.23.0

• bioconductor-genomicalignments >=1.22.0,<1.23.0

• bioconductor-genomicfeatures >=1.38.0,<1.39.0

• bioconductor-genomicranges >=1.38.0,<1.39.0

• bioconductor-gviz >=1.30.0,<1.31.0

• bioconductor-iranges >=2.20.0,<2.21.0

• bioconductor-rsamtools >=2.2.0,<2.3.0

• bioconductor-rtracklayer >=1.46.0,<1.47.0

• bioconductor-s4vectors >=0.24.0,<0.25.0

• bioconductor-summarizedexperiment >=1.16.0,<1.17.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

• 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)