- recipe bioconductor-fcbf
Fast Correlation Based Filter for Feature Selection
- Homepage:
- License:
MIT + file LICENSE
- Recipe:
This package provides a simple R implementation for the Fast Correlation Based Filter described in Yu, L. and Liu, H.; Feature Selection for High-Dimensional Data: A Fast Correlation Based Filter Solution,Proc. 20th Intl. Conf. Mach. Learn. (ICML-2003), Washington DC, 2003 The current package is an intent to make easier for bioinformaticians to use FCBF for feature selection, especially regarding transcriptomic data.This implies discretizing expression (function discretize_exprs) before calculating the features that explain the class, but are not predictable by other features. The functions are implemented based on the algorithm of Yu and Liu, 2003 and Rajarshi Guha's implementation from 13/05/2005 available (as of 26/08/2018) at http://www.rguha.net/code/R/fcbf.R .
- package bioconductor-fcbf¶
- Versions:
2.8.0-0,2.6.0-0,2.2.0-0,2.0.0-0,1.8.0-1,1.8.0-0,1.6.0-0,1.4.0-0,1.2.2-0,2.8.0-0,2.6.0-0,2.2.0-0,2.0.0-0,1.8.0-1,1.8.0-0,1.6.0-0,1.4.0-0,1.2.2-0,1.0.1-0,1.0.0-0- Depends:
on bioconductor-summarizedexperiment
>=1.30.0,<1.31.0on r-base
>=4.3,<4.4.0a0on r-ggplot2
on r-gridextra
on r-mclust
on r-pbapply
- 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-fcbf
to add into an existing workspace instead, run:
pixi add bioconductor-fcbf
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-fcbf
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-fcbf
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-fcbf:<tag>
(see bioconductor-fcbf/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-fcbf/README.html)
