Package Recipe 'bioconductor-genextender'

recipe bioconductor-genextender

Optimized Functional Annotation Of ChIP-seq Data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/geneXtendeR.html
License:: GPL (>= 3)
Recipe:: /bioconductor-genextender/meta.yaml
Links:: biotools: genextender

geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, …, n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.

package bioconductor-genextender¶

Versions:

1.36.0-1, 1.32.0-0, 1.28.0-1, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.24.0-0, 1.20.0-2, 1.20.0-1,

1.36.0-1, 1.32.0-0, 1.28.0-1, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.24.0-0, 1.20.0-2, 1.20.0-1, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.11.0-0, 1.10.0-1, 1.8.0-0

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-annotationdbi >=1.72.0,<1.73.0a0
on bioconductor-biocstyle >=2.38.0,<2.39.0
on bioconductor-biocstyle >=2.38.0,<2.39.0a0
on bioconductor-go.db >=3.22.0,<3.23.0
on bioconductor-go.db >=3.22.0,<3.23.0a0
on bioconductor-org.rn.eg.db >=3.22.0,<3.23.0
on bioconductor-org.rn.eg.db >=3.22.0,<3.23.0a0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-rtracklayer >=1.70.1,<1.71.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dplyr
on r-networkd3
on r-rcolorbrewer
on r-snowballc
on r-tm
on r-wordcloud

Additional platforms:

linux-aarch64

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-genextender

to add into an existing workspace instead, run:

pixi add bioconductor-genextender

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-genextender

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-genextender

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-genextender:<tag>

(see bioconductor-genextender/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-genextender/README.html)