- recipe bioconductor-rtcga
The Cancer Genome Atlas Data Integration
- Homepage:
- License:
GPL-2
- Recipe:
- Links:
biotools: rtcga, doi: 10.1038/nmeth.3252
The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.
- package bioconductor-rtcga¶
- Versions:
1.40.0-0,1.36.0-0,1.32.0-0,1.30.0-0,1.28.0-0,1.24.0-0,1.22.0-0,1.20.0-1,1.20.0-0,1.40.0-0,1.36.0-0,1.32.0-0,1.30.0-0,1.28.0-0,1.24.0-0,1.22.0-0,1.20.0-1,1.20.0-0,1.18.0-0,1.16.0-0,1.14.0-1,1.14.0-0,1.12.1-0,1.10.0-0,1.8.0-0- Depends:
on r-assertthat
on r-base
>=4.5,<4.6.0a0on r-data.table
on r-dplyr
on r-ggplot2
on r-ggthemes
on r-htmltools
on r-knitr
on r-purrr
on r-rcurl
on r-rmarkdown
on r-rvest
on r-scales
on r-stringi
on r-survival
on r-survminer
on r-viridis
on r-xml
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-rtcga
to add into an existing workspace instead, run:
pixi add bioconductor-rtcga
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-rtcga
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-rtcga
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-rtcga:<tag>
(see bioconductor-rtcga/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:
[](http://bioconda.github.io/recipes/bioconductor-rtcga/README.html)
