qubic's Introduction

QUBIC

Desription

QUBIC is recognized as one of the best biclustering methods in terms of its efficiency and effetiveness in biological data interpretion. This package provides an R implementation of the QUBIC algorithm, with significantly improved efficiency and comprehensive functions.

Installation

Please follow the instructions mentioned in the URL: http://bioconductor.org/packages/QUBIC

To install the development version of QUBIC, you will need to install at least the following packages from CRAN

install.packages("biclust")
install.packages("Rcpp")
install.packages("RcppArmadillo")
source("http://bioconductor.org/biocLite.R") # install BiocInstaller

For Windows users, Rtools(https://cran.r-project.org/bin/windows/Rtools/) should also be installed.

Then,

install.packages("devtools")
devtools::install_github("zy26/QUBIC")

To draw heatmap and visualize network, the following packages should also be installed:

install.packages("qgraph")
install.packages("RcolorBrewer")

Vignette

You can find the tutorial for QUBIC at https://bioconductor.org/packages/release/bioc/vignettes/QUBIC/inst/doc/qubic_vignette.pdf

qubic's People

Contributors

Stargazers

Watchers

qubic's Issues

cluster.cc compilation failed

Hi,

I tried installing QUBIC following the instructions here http://bioconductor.org/packages/release/bioc/html/QUBIC.html using gcc v6.2.0 and R v3.4.1. It first compiles RcppExports.cpp and charset.cc successfully, but will then return the following errors when compiling cluster.cc

cluster.cc: In function 'std::vector cluster(const DiscreteArrayListWithSymbols&, const std::vector<Edge*>&, std::size_t, double, bool, bool, bool, std::size_t, int, double, double, bool)':
cluster.cc:381:29: error: 'stdout' was not declared in this scope
if (verbose) fputc('.', stdout);
^~~~~~
cluster.cc:381:35: error: 'fputc' was not declared in this scope
if (verbose) fputc('.', stdout);
^
cluster.cc:383:24: error: 'stdout' was not declared in this scope
if (verbose) fprintf(stdout, "\n");
^~~~~~
cluster.cc:383:36: error: 'fprintf' was not declared in this scope
if (verbose) fprintf(stdout, "\n");
^
make: *** [cluster.o] Error 1
ERROR: compilation failed for package 'QUBIC'

Could you please help me troubleshoot this?

Thank you very much.

Recommend Projects