recipe bioconductor-tcgabiolinks

TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-tcgabiolinks/meta.yaml

Links:

biotools: tcgabiolinks, doi: 10.1093/nar/gkv1507

The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

package bioconductor-tcgabiolinks

versions:

2.28.3-0,  2.25.3-0,  2.22.1-0,  2.20.0-0,  2.18.0-1,  2.18.0-0,  2.16.0-0,  2.14.0-0,  2.12.3-0, 

2.28.3-0,  2.25.3-0,  2.22.1-0,  2.20.0-0,  2.18.0-1,  2.18.0-0,  2.16.0-0,  2.14.0-0,  2.12.3-0,  2.10.0-0,  2.8.4-0,  2.6.11-0

depends bioconductor-biomart:

>=2.56.0,<2.57.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends bioconductor-tcgabiolinksgui.data:

>=1.20.0,<1.21.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-downloader:

>=0.4

depends r-dplyr:

depends r-ggplot2:

depends r-httr:

>=1.2.1

depends r-jsonlite:

>=1.0.0

depends r-knitr:

depends r-plyr:

depends r-purrr:

depends r-r.utils:

depends r-readr:

depends r-rvest:

>=0.3.0

depends r-stringr:

>=1.0.0

depends r-tibble:

depends r-tidyr:

depends r-xml:

>=3.98.0

depends r-xml2:

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-tcgabiolinks

and update with::

   mamba update bioconductor-tcgabiolinks

To create a new environment, run:

mamba create --name myenvname bioconductor-tcgabiolinks

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-tcgabiolinks:<tag>

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

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