recipe bioconductor-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.



GPL (>= 3)



package bioconductor-genextender

(downloads) docker_bioconductor-genextender



Required By


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-genextender

and update with:

conda update bioconductor-genextender

or use the docker container:

docker pull<tag>

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