recipe bioconductor-proactiv

Estimate Promoter Activity from RNA-Seq data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/proActiv.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-proactiv/meta.yaml

Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.

package bioconductor-proactiv

Versions:

1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-dplyr

• r-ggplot2

• r-gplots

• r-rlang

• r-scales

• r-tibble

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-proactiv

and update with:

conda update bioconductor-proactiv

or use the docker container:

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

(see bioconductor-proactiv/tags for valid values for <tag>)

Download stats

Link to this page

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