recipe bioconductor-nadfinder

Call wide peaks for sequencing data

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-nadfinder/meta.yaml

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

Versions:

1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.1-0,  1.6.0-0, 

1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.1-0,  1.6.0-0,  1.4.0-0,  1.2.0-0

Depends:

• bioconductor-atacseqqc >=1.22.0,<1.23.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-csaw >=1.32.0,<1.33.0

• bioconductor-empiricalbrownsmethod >=1.26.0,<1.27.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-trackviewer >=1.34.0,<1.35.0

• r-base >=4.2,<4.3.0a0

• r-baseline

• r-corrplot

• r-metap

• r-signal

Required By:

Installation

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

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

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