recipe bioconductor-uncoverapplib

Interactive graphical application for clinical assessment of sequence coverage at the base-pair level

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/uncoverappLib.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-uncoverapplib/meta.yaml

a Shiny application containing a suite of graphical and statistical tools to support clinical assessment of low coverage regions.It displays three web pages each providing a different analysis module: Coverage analysis, calculate AF by allele frequency app and binomial distribution. uncoverAPP provides a statisticl summary of coverage given target file or genes name.

package bioconductor-uncoverapplib

versions:

1.12.0-0,  1.10.0-0,  1.7.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-ensdb.hsapiens.v75:

>=2.99.0,<2.100.0

depends bioconductor-ensdb.hsapiens.v86:

>=2.99.0,<2.100.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-gviz:

>=1.46.0,<1.47.0

depends bioconductor-homo.sapiens:

>=1.3.0,<1.4.0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends bioconductor-organismdbi:

>=1.44.0,<1.45.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:

>=3.2.0,<3.3.0

depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:

>=3.18.0,<3.19.0

depends r-base:

>=4.3,<4.4.0a0

depends r-condformat:

depends r-dt:

depends r-markdown:

depends r-openxlsx:

depends r-processx:

depends r-rappdirs:

depends r-rlist:

depends r-shiny:

depends r-shinybs:

depends r-shinycssloaders:

depends r-shinyjs:

depends r-shinywidgets:

depends r-stringr:

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-uncoverapplib

and update with::

   mamba update bioconductor-uncoverapplib

To create a new environment, run:

mamba create --name myenvname bioconductor-uncoverapplib

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-uncoverapplib:<tag>

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

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