- recipe bioconductor-extrachips
Additional functions for working with ChIP-Seq data
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/extraChIPs.html
- License:
GPL-3
- Recipe:
This package builds on existing tools and adds some simple but extremely useful capabilities for working wth 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:
1.6.0-0,1.4.5-0,1.2.0-0- depends bioconductor-biocio:
>=1.12.0,<1.13.0- depends bioconductor-biocio:
>=1.12.0,<1.13.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-csaw:
>=1.36.0,<1.37.0- depends bioconductor-csaw:
>=1.36.0,<1.37.0a0- depends bioconductor-edger:
>=4.0.0,<4.1.0- depends bioconductor-edger:
>=4.0.2,<4.1.0a0- depends bioconductor-enrichedheatmap:
>=1.32.0,<1.33.0- depends bioconductor-enrichedheatmap:
>=1.32.0,<1.33.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicinteractions:
>=1.36.0,<1.37.0- depends bioconductor-genomicinteractions:
>=1.36.0,<1.37.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-gviz:
>=1.46.0,<1.47.0- depends bioconductor-gviz:
>=1.46.1,<1.47.0a0- depends bioconductor-interactionset:
>=1.30.0,<1.31.0- depends bioconductor-interactionset:
>=1.30.0,<1.31.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-limma:
>=3.58.0,<3.59.0- depends bioconductor-limma:
>=3.58.1,<3.59.0a0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0a0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends r-base:
>=4.3,<4.4.0a0- depends r-broom:
- depends r-complexupset:
- depends r-dplyr:
>=1.1.1- depends r-forcats:
- depends r-ggforce:
- depends r-ggplot2:
>=3.4.0- depends r-ggrepel:
- depends r-ggside:
>=0.2.2- depends r-glue:
- depends r-matrixstats:
- depends r-patchwork:
- depends r-rcolorbrewer:
- depends r-rlang:
- depends r-scales:
- depends r-stringr:
- depends r-tibble:
- depends r-tidyr:
- depends r-tidyselect:
- depends r-vctrs:
- depends r-venndiagram:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-extrachips and update with:: mamba update bioconductor-extrachips
To create a new environment, run:
mamba create --name myenvname bioconductor-extrachips
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-extrachips:<tag> (see `bioconductor-extrachips/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-extrachips/README.html)
