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/3.11/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

1.22.0-0,  1.20.0-0,  1.18.3-0,  1.16.1-0,  1.14.0-0,  1.12.0-0

Depends

• bioconductor-annotationdbi >=1.50.0,<1.51.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-bumphunter >=1.30.0,<1.31.0

• bioconductor-derfinderhelper >=1.22.0,<1.23.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicalignments >=1.24.0,<1.25.0

• bioconductor-genomicfeatures >=1.40.0,<1.41.0

• bioconductor-genomicfiles >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-qvalue >=2.20.0,<2.21.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• r-base >=4.0,<4.1.0a0

• r-hmisc

Required By

• bioconductor-recount

• bioconductor-brainflowprobes

• bioconductor-genomicstate

• bioconductor-derfinderplot

• bioconductor-regionreport

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:

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