Package Recipe 'bioconductor-chipseeker'

recipe bioconductor-chipseeker

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

Homepage:: https://bioconductor.org/packages/3.20/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:

1.46.1-0, 1.42.0-0, 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,

1.46.1-0, 1.42.0-0, 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:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-enrichplot >=1.30.0,<1.31.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.22.0,<3.23.0
on r-aplot
on r-base >=4.5,<4.6.0a0
on r-boot
on r-dplyr
on r-ggplot2
on r-gplots
on r-gtools
on r-magrittr
on r-plotrix
on r-rcolorbrewer
on r-rlang
on r-scales
on r-tibble
on r-yulab.utils >=0.2.0

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-chipseeker

to add into an existing workspace instead, run:

pixi add bioconductor-chipseeker

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-chipseeker

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-chipseeker

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-chipseeker/README.html)