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/3.14/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:

1.28.0-0,  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, 

1.28.0-0,  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 >=1.56.0,<1.57.0

• bioconductor-biocgenerics >=0.40.0,<0.41.0

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-bumphunter >=1.36.0,<1.37.0

• bioconductor-derfinderhelper >=1.28.0,<1.29.0

• bioconductor-genomeinfodb >=1.30.0,<1.31.0

• bioconductor-genomicalignments >=1.30.0,<1.31.0

• bioconductor-genomicfeatures >=1.46.0,<1.47.0

• bioconductor-genomicfiles >=1.30.0,<1.31.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-qvalue >=2.26.0,<2.27.0

• bioconductor-rsamtools >=2.10.0,<2.11.0

• bioconductor-rtracklayer >=1.54.0,<1.55.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• r-base >=4.1,<4.2.0a0

• r-hmisc

Required By:

• bioconductor-derfinderplot

• bioconductor-regionreport

• bioconductor-oder

• bioconductor-brainflowprobes

• bioconductor-recount

• bioconductor-genomicstate

Installation

With an activated Bioconda channel (see 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>)

Download stats

Link to this page

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