recipe bioconductor-chipseeker

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/ChIPseeker.html

License:

Artistic-2.0

Recipe:

/bioconductor-chipseeker/meta.yaml

Links:

biotools: chipseeker

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

package bioconductor-chipseeker

versions:

1.38.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.28.3-1,  1.28.3-0,  1.26.2-0,  1.26.0-0, 

1.38.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.28.3-1,  1.28.3-0,  1.26.2-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.18.0-0,  1.16.1-0,  1.14.2-0,  1.14.0-0,  1.12.1-0,  1.10.0-0,  1.6.6-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-enrichplot:

>=1.22.0,<1.23.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:

>=3.2.0,<3.3.0

depends r-aplot:

depends r-base:

>=4.3,<4.4.0a0

depends r-boot:

depends r-dplyr:

depends r-ggplot2:

depends r-gplots:

depends r-gtools:

depends r-magrittr:

depends r-plotrix:

depends r-tibble:

depends r-yulab.utils:

requirements:

additional platforms:

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-chipseeker

and update with::

   mamba update bioconductor-chipseeker

To create a new environment, run:

mamba create --name myenvname bioconductor-chipseeker

with myenvname being 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-chipseeker:<tag>

(see `bioconductor-chipseeker/tags`_ for valid values for ``<tag>``)

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