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bioconductor-qubic

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

Installation

To install this package, run one of the following:

Conda
$conda install bioconda::bioconductor-qubic

Usage Tracking

1.34.0
1.30.0
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1.26.0
1.22.0
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Downloads (Last 6 months): 0

Description

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).

About

Summary

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

Last Updated

Dec 14, 2024 at 18:26

License

CC BY-NC-ND 4.0 + file LICENSE

Total Downloads

32.4K

Supported Platforms

linux-64
macOS-64