recipe bioconductor-extrachips

Additional functions for working with ChIP-Seq data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-extrachips/meta.yaml

This package builds on existing tools and adds some simple but extremely useful capabilities for working with ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also included.

package bioconductor-extrachips

Versions:

1.2.0-0

Depends:

• bioconductor-biocio >=1.8.0,<1.9.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-csaw >=1.32.0,<1.33.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-enrichedheatmap >=1.27.0,<1.28.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicinteractions >=1.32.0,<1.33.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-gviz >=1.42.0,<1.43.0

• bioconductor-interactionset >=1.26.0,<1.27.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-broom

• r-complexupset

• r-dplyr

• r-forcats

• r-ggforce

• r-ggplot2

• r-ggrepel

• r-ggside

• r-glue

• r-rcolorbrewer

• r-rlang

• r-scales

• r-stringr

• r-tibble

• r-tidyr

• r-tidyselect

• r-vctrs

• r-venndiagram

Required By:

Installation

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

conda install bioconductor-extrachips

and update with:

conda update bioconductor-extrachips

or use the docker container:

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

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

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Link to this page

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