recipe bioconductor-derfinder

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

Homepage

https://bioconductor.org/packages/3.10/bioc/html/derfinder.html

License

Artistic-2.0

Recipe

/bioconductor-derfinder/meta.yaml

Links

biotools: derfinder

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.

package bioconductor-derfinder

Versions

1.20.0-0, 1.18.3-0, 1.16.1-0, 1.14.0-0, 1.12.0-0

Depends

• bioconductor-annotationdbi >=1.48.0,<1.49.0

• bioconductor-biocgenerics >=0.32.0,<0.33.0

• bioconductor-biocparallel >=1.20.0,<1.21.0

• bioconductor-bumphunter >=1.28.0,<1.29.0

• bioconductor-derfinderhelper >=1.20.0,<1.21.0

• 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-genomicfiles >=1.22.0,<1.23.0

• bioconductor-genomicranges >=1.38.0,<1.39.0

• bioconductor-iranges >=2.20.0,<2.21.0

• bioconductor-qvalue >=2.18.0,<2.19.0

• bioconductor-rsamtools >=2.2.0,<2.3.0

• bioconductor-rtracklayer >=1.46.0,<1.47.0

• bioconductor-s4vectors >=0.24.0,<0.25.0

• r-base >=3.6,<3.7.0a0

• r-hmisc

Required By

• bioconductor-regionreport

• bioconductor-derfinderplot

• bioconductor-recount

Installation

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

conda install bioconductor-derfinder

and update with:

conda update bioconductor-derfinder

or use the docker container:

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

(see bioconductor-derfinder/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-derfinder/README.html)