recipe bioconductor-recoup

An R package for the creation of complex genomic profile plots

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-recoup/meta.yaml

Links:

biotools: recoup, doi: 10.1038/nmeth.3252

recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.

package bioconductor-recoup

Versions:

1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-0, 

1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biomart >=2.54.0,<2.55.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-complexheatmap >=2.14.0,<2.15.0

• 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-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

• r-circlize

• r-ggplot2

• r-httr

• r-rsqlite

• r-stringr

Required By:

Installation

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

conda install bioconductor-recoup

and update with:

conda update bioconductor-recoup

or use the docker container:

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

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

Download stats

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