Package: QUBIC 1.33.0
Yu Zhang
QUBIC: An R package for qualitative biclustering in support of gene co-expression analyses
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).
Authors:
QUBIC_1.33.0.tar.gz
QUBIC_1.33.0.zip(r-4.5)QUBIC_1.33.0.zip(r-4.4)QUBIC_1.33.0.zip(r-4.3)
QUBIC_1.33.0.tgz(r-4.4-arm64)QUBIC_1.33.0.tgz(r-4.4-x86_64)QUBIC_1.33.0.tgz(r-4.3-arm64)QUBIC_1.33.0.tgz(r-4.3-x86_64)
QUBIC_1.33.0.tar.gz(r-4.5-noble)QUBIC_1.33.0.tar.gz(r-4.4-noble)
QUBIC_1.33.0.tgz(r-4.4-emscripten)QUBIC_1.33.0.tgz(r-4.3-emscripten)
QUBIC.pdf |QUBIC.html✨
QUBIC/json (API)
NEWS
| # Install 'QUBIC' in R: |
| install.packages('QUBIC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zy26/qubic/issues
On BioConductor:QUBIC-1.33.0(bioc 3.20)QUBIC-1.32.0(bioc 3.19)
Last updated 2 months agofrom:4b9a64e3df
Exports:BCQUBCQUDqubiclustqubiclust_dqudiscretizequheatmapqunet2xmlqunetworkshowinfo
Dependencies:additivityTestsbiclustclassclicolorspacecpp11dplyrfansifarverflexclustgenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmodeltoolsmunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcppRcppArmadillorlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class BCQU. | BCQU-class |
| QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data | BCQU bcqu BCQUD BCQUD-class biclust,matrix,BCQU-method biclust,matrix,BCQUD-method QUBIC qubic QUBICD qubiclust qubiclust_d qubic_d QUD |
| Create a qualitative discrete matrix for a given gene expression matrix | qdiscretize qudiscretize |
| Visualization of identified biclusters | quheatmap |
| Convert newwork to XGMML | qunet2xml |
| Construction and visualization of co-expression network | network Qnetwork Qunetwork qunetwork |
| Show report of biclusters | showinfo |
