recipe bioconductor-nadfinder

Call wide peaks for sequencing data



GPL (>= 2)



Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including baseline correction, smoothing, normalization, peak calling, and annotation.

package bioconductor-nadfinder

(downloads) docker_bioconductor-nadfinder



Required By:


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

conda install bioconductor-nadfinder

and update with:

conda update bioconductor-nadfinder

or use the docker container:

docker pull<tag>

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

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