Package Recipe 'bioconductor-cola'

recipe bioconductor-cola

A Framework for Consensus Partitioning

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/cola.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-cola/meta.yaml

Subgroup classification is a basic task in genomic data analysis, especially for gene expression and DNA methylation data analysis. It can also be used to test the agreement to known clinical annotations, or to test whether there exist significant batch effects. The cola package provides a general framework for subgroup classification by consensus partitioning. It has the following features: 1. It modularizes the consensus partitioning processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to straightforward compare results. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It automatically generates detailed reports for the complete analysis. 6. It allows applying consensus partitioning in a hierarchical manner.

package bioconductor-cola¶

Versions:

2.16.1-0, 2.12.0-0, 2.8.0-0, 2.6.0-0, 2.4.0-1, 2.4.0-0, 2.0.0-2, 2.0.0-1, 2.0.0-0,

2.16.1-0, 2.12.0-0, 2.8.0-0, 2.6.0-0, 2.4.0-1, 2.4.0-0, 2.0.0-2, 2.0.0-1, 2.0.0-0, 1.8.0-0, 1.6.0-1, 1.6.0-0, 1.4.1-0, 1.2.0-0, 1.0.0-1, 1.0.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-complexheatmap >=2.26.1,<2.27.0a0
on bioconductor-impute >=1.84.0,<1.85.0
on bioconductor-impute >=1.84.0,<1.85.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-brew
on r-circlize >=0.4.7
on r-clue
on r-cluster
on r-crayon
on r-digest
on r-doparallel
on r-dorng
on r-eulerr
on r-foreach
on r-getoptlong
on r-globaloptions >=0.1.0
on r-httr
on r-irlba
on r-knitr >=1.4.0
on r-markdown >=1.6
on r-matrixstats >=1.2.0
on r-mclust
on r-microbenchmark
on r-png
on r-rcolorbrewer
on r-rcpp >=0.11.0
on r-skmeans
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-cola

to add into an existing workspace instead, run:

pixi add bioconductor-cola

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-cola

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cola

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-cola:<tag>

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