recipe bioconductor-srnadiff

Finding differentially expressed unannotated genomic regions from RNA-seq data

Homepage

https://bioconductor.org/packages/3.13/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. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.

package bioconductor-srnadiff

Versions

1.12.2-0,  1.11.0-0,  1.10.1-0,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

Depends

• bioconductor-bayseq >=2.26.0,<2.27.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-biocstyle >=2.20.0,<2.21.0

• bioconductor-deseq2 >=1.32.0,<1.33.0

• bioconductor-edger >=3.34.0,<3.35.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomicalignments >=1.28.0,<1.29.0

• bioconductor-genomicfeatures >=1.44.0,<1.45.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-gviz >=1.36.0,<1.37.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-rtracklayer >=1.52.0,<1.53.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=9.3.0

• r-base >=4.1,<4.2.0a0

• 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>)

Download stats

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)