Package Recipe 'bioconductor-tcgautils'

recipe bioconductor-tcgautils

TCGA utility functions for data management

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/TCGAutils.html
License:: Artistic-2.0
Recipe:: /bioconductor-tcgautils/meta.yaml

A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

package bioconductor-tcgautils¶

Versions:

1.30.2-0, 1.26.0-0, 1.22.0-0, 1.20.2-0, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0,

1.30.2-0, 1.26.0-0, 1.22.0-0, 1.20.2-0, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.2.1-0

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-biocbaseutils >=1.12.0,<1.13.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicdatacommons >=1.34.0,<1.35.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-multiassayexperiment >=1.36.0,<1.37.0
on bioconductor-raggedexperiment >=1.34.0,<1.35.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-rvest
on r-stringr
on r-xml2

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-tcgautils

to add into an existing workspace instead, run:

pixi add bioconductor-tcgautils

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-tcgautils

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-tcgautils

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-tcgautils:<tag>

(see bioconductor-tcgautils/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-tcgautils/README.html)