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

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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).

Author
Yu Zhang [aut, cre], Qin Ma [aut]
Date of publication
None
Maintainer
Yu Zhang <zy26@jlu.edu.cn>
License
CC BY-NC-ND 4.0 + file LICENSE
Version
1.2.0
URLs

View on Bioconductor

Man pages

BCQU-class
Class BCQU.
QUBIC
QUBIC: A Qualitative Biclustering Algorithm for Analyses of...
qudiscretize
Create a qualitative discrete matrix for a given gene...
quheatmap
Visualization of identified biclusters
qunet2xml
Convert newwork to XGMML
qunetwork
Construction and visualization of co-expression network
showinfo
Show report of biclusters

Files in this package

QUBIC/DESCRIPTION
QUBIC/LICENSE
QUBIC/NAMESPACE
QUBIC/R
QUBIC/R/RcppExports.R
QUBIC/R/aaa-qubic.R
QUBIC/R/qubiclust.R
QUBIC/R/quheatmap.R
QUBIC/R/qunet2xml.R
QUBIC/R/qunetwork.R
QUBIC/R/showinfo.R
QUBIC/build
QUBIC/build/vignette.rds
QUBIC/inst
QUBIC/inst/NEWS.Rd
QUBIC/inst/doc
QUBIC/inst/doc/qubic_vignette.R
QUBIC/inst/doc/qubic_vignette.Rmd
QUBIC/inst/doc/qubic_vignette.pdf
QUBIC/man
QUBIC/man/BCQU-class.Rd
QUBIC/man/QUBIC.Rd
QUBIC/man/qudiscretize.Rd
QUBIC/man/quheatmap.Rd
QUBIC/man/qunet2xml.Rd
QUBIC/man/qunetwork.Rd
QUBIC/man/showinfo.Rd
QUBIC/src
QUBIC/src/Makevars
QUBIC/src/Makevars.win
QUBIC/src/RcppExports.cpp
QUBIC/src/block.h
QUBIC/src/charset.cc
QUBIC/src/charset.h
QUBIC/src/cluster.cc
QUBIC/src/cluster.h
QUBIC/src/config.h
QUBIC/src/discrete.h
QUBIC/src/discretize.cc
QUBIC/src/discretize.h
QUBIC/src/edge_list.cc
QUBIC/src/edge_list.h
QUBIC/src/fib.c
QUBIC/src/fib.h
QUBIC/src/fibpriv.h
QUBIC/src/fopen_matrix.cc
QUBIC/src/fopen_matrix.h
QUBIC/src/fstream_matrix.h
QUBIC/src/matrix.h
QUBIC/src/matrix_float.h
QUBIC/src/option.h
QUBIC/src/qubic.cc
QUBIC/src/qubic.h
QUBIC/src/rcpp_qubic.cpp
QUBIC/src/struct.cc
QUBIC/src/struct.h
QUBIC/src/version.h
QUBIC/vignettes
QUBIC/vignettes/bibliography.bib
QUBIC/vignettes/qubic_vignette.Rmd