recipe bioconductor-trackviewer

A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/trackViewer.html

License:

GPL (>= 2)

Recipe:

/bioconductor-trackviewer/meta.yaml

Links:

biotools: trackviewer, doi: 10.1038/nmeth.3252

Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

package bioconductor-trackviewer

versions:

1.36.2-0,  1.34.0-1,  1.34.0-0,  1.30.0-2,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.2-0,  1.26.0-0, 

1.36.2-0,  1.34.0-1,  1.34.0-0,  1.30.0-2,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.2-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.5-0,  1.18.0-1,  1.18.0-0,  1.16.1-0,  1.14.1-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicalignments:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-graph:

>=1.78.0,<1.79.0

depends bioconductor-gviz:

>=1.44.0,<1.45.0

depends bioconductor-interactionset:

>=1.28.0,<1.29.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rgraphviz:

>=2.44.0,<2.45.0

depends bioconductor-rhdf5:

>=2.44.0,<2.45.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends r-base:

>=4.3,<4.4.0a0

depends r-grimport:

depends r-htmlwidgets:

depends r-plotrix:

depends r-scales:

depends r-strawr:

requirements:

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-trackviewer

and update with::

   mamba update bioconductor-trackviewer

To create a new environment, run:

mamba create --name myenvname bioconductor-trackviewer

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-trackviewer:<tag>

(see `bioconductor-trackviewer/tags`_ for valid values for ``<tag>``)

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