Package Recipe 'bioconductor-uncoverapplib'

recipe bioconductor-uncoverapplib

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

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

1.20.0-0, 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:

on bioconductor-biocfilecache >=3.0.0,<3.1.0
on bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0
on bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-gviz >=1.54.0,<1.55.0
on bioconductor-homo.sapiens >=1.3.0,<1.4.0
on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0
on bioconductor-organismdbi >=1.52.0,<1.53.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.22.0,<3.23.0
on bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.22.0,<3.23.0
on r-base >=4.5,<4.6.0a0
on r-condformat
on r-dt
on r-markdown
on r-openxlsx
on r-processx
on r-rappdirs
on r-rlist
on r-shiny
on r-shinybs
on r-shinycssloaders
on r-shinyjs
on r-shinywidgets
on r-stringr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-uncoverapplib

to add into an existing workspace instead, run:

pixi add bioconductor-uncoverapplib

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-uncoverapplib

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-uncoverapplib

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-uncoverapplib/README.html)