recipe bioconductor-nadfinder

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 normalization, smoothing, peak calling, peak trimming and annotation.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/NADfinder.html

License

GPL (>= 2)

Recipe

/bioconductor-nadfinder/meta.yaml

package bioconductor-nadfinder

(downloads) docker_bioconductor-nadfinder

Versions

1.6.0-0, 1.4.0-0, 1.2.0-0

Depends bioconductor-atacseqqc

>=1.6.0,<1.7.0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-csaw

>=1.16.0,<1.17.0

Depends bioconductor-empiricalbrownsmethod

>=1.10.0,<1.11.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicalignments

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-rtracklayer

>=1.42.0,<1.43.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends bioconductor-trackviewer

>=1.18.0,<1.19.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-baseline

Depends r-corrplot

Depends r-metap

Depends r-rbamtools

Depends r-signal

Requirements

Installation

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

conda install bioconductor-nadfinder

and update with:

conda update bioconductor-nadfinder

or use the docker container:

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

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