recipe bioconductor-qubic

An R package for qualitative biclustering in support of gene co-expression analyses

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/QUBIC.html

License:

CC BY-NC-ND 4.0 + file LICENSE

Recipe:

/bioconductor-qubic/meta.yaml

The core function of this R package is to provide the implementation of the well-cited and well-reviewed QUBIC algorithm, aiming to deliver an effective and efficient biclustering capability. This package also includes the following related functions: (i) a qualitative representation of the input gene expression data, through a well-designed discretization way considering the underlying data property, which can be directly used in other biclustering programs; (ii) visualization of identified biclusters using heatmap in support of overall expression pattern analysis; (iii) bicluster-based co-expression network elucidation and visualization, where different correlation coefficient scores between a pair of genes are provided; and (iv) a generalize output format of biclusters and corresponding network can be freely downloaded so that a user can easily do following comprehensive functional enrichment analysis (e.g. DAVID) and advanced network visualization (e.g. Cytoscape).

package bioconductor-qubic

Versions:

1.26.0-0,  1.22.0-2,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0, 

1.26.0-0,  1.22.0-2,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0

Depends:

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-biclust

• r-matrix

• r-rcpp >=0.11.0

• r-rcpparmadillo

Required By:

• bioconductor-mosbi

Installation

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

conda install bioconductor-qubic

and update with:

conda update bioconductor-qubic

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-qubic:<tag>

(see bioconductor-qubic/tags for valid values for <tag>)

Download stats

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