recipe bioconductor-nadfinder

Call wide peaks for sequencing data

Homepage:

https://bioconductor.org/packages/3.20/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:

1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0, 

1.30.0-0,  1.26.0-0,  1.24.0-0,  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:

>=1.30.0,<1.31.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-csaw:

>=1.40.0,<1.41.0

depends bioconductor-empiricalbrownsmethod:

>=1.34.0,<1.35.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicalignments:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-trackviewer:

>=1.42.0,<1.43.0

depends r-base:

>=4.4,<4.5.0a0

depends r-baseline:

depends r-corrplot:

depends r-metap:

depends r-signal:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-nadfinder

and update with::

   mamba update bioconductor-nadfinder

To create a new environment, run:

mamba create --name myenvname bioconductor-nadfinder

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, 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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