recipe bioconductor-genextender

Optimized Functional Annotation Of ChIP-seq Data

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-genextender/meta.yaml

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:

1.24.0-0,  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, 

1.24.0-0,  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:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biocstyle >=2.26.0,<2.27.0

• bioconductor-go.db >=3.16.0,<3.17.0

• bioconductor-org.rn.eg.db >=3.16.0,<3.17.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-dplyr

• r-networkd3

• r-rcolorbrewer

• r-snowballc

• r-tm

• r-wordcloud

Required By:

Installation

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

conda install bioconductor-genextender

and update with:

conda update bioconductor-genextender

or use the docker container:

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

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

Download stats

Link to this page

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