recipe bioconductor-tcgabiolinks

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

Homepage:

https://bioconductor.org/packages/3.16/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:

2.25.3-0,  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, 

2.25.3-0,  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 >=2.54.0,<2.55.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-tcgabiolinksgui.data >=1.18.0,<1.19.0

• r-base >=4.2,<4.3.0a0

• r-data.table

• r-downloader >=0.4

• r-dplyr

• r-ggplot2

• r-httr >=1.2.1

• r-jsonlite >=1.0.0

• r-knitr

• r-plyr

• r-purrr

• r-r.utils

• r-readr

• r-rvest >=0.3.0

• r-stringr >=1.0.0

• r-tibble

• r-tidyr

• r-xml >=3.98.0

• r-xml2

Required By:

• bioconductor-tcgabiolinksgui

• bioconductor-moonlightr

• bioconductor-elmer

• bioconductor-mirlab

• bioconductor-musicatk

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-tcgabiolinks

and update with:

conda update bioconductor-tcgabiolinks

or 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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