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/3.13/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

1.26.0-0,  1.24.2-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.3-0,  1.16.1-0,  1.14.0-0,  1.12.0-0

Depends

• bioconductor-annotationdbi >=1.54.0,<1.55.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-bumphunter >=1.34.0,<1.35.0

• bioconductor-derfinderhelper >=1.26.0,<1.27.0

• 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-genomicfiles >=1.28.0,<1.29.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-qvalue >=2.24.0,<2.25.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-rtracklayer >=1.52.0,<1.53.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• r-base >=4.1,<4.2.0a0

• r-hmisc

Required By

• bioconductor-recount

• bioconductor-genomicstate

• bioconductor-brainflowprobes

• bioconductor-regionreport

• bioconductor-derfinderplot

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)