rsgcc: Gini methodology-based correlation and clustering analysis of microarray and RNA-Seq gene expression data
Version 1.0.6

This package provides functions for calculating associations between two genes with five correlation methods(e.g., the Gini correlation coefficient [GCC], the Pearson's product moment correlation coefficient [PCC], the Kendall tau rank correlation coefficient [KCC], the Spearman's rank correlation coefficient [SCC] and the Tukey's biweight correlation coefficient [BiWt], and three non-correlation methods (e.g., mutual information [MI] and the maximal information-based nonparametric exploration [MINE], and the euclidean distance [ED]). It can also been implemented to perform the correlation and clustering analysis of transcriptomic data profiled by microarray and RNA-Seq technologies. Additionally, this package can be further applied to construct gene co-expression networks (GCNs).

AuthorChuang Ma, Xiangfeng Wang
Date of publication2013-06-18 07:40:43
MaintainerChuang Ma <chuangma2006@gmail.com>
LicenseGPL (>= 2)
Version1.0.6
URL http://www.cmbb.arizona.edu/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rsgcc")

Getting started

Package overview

Popular man pages

cor.matrix: correlation calculation for a set of genes
data: example of RNA-Seq gene expression data
gcc.hclust: hierarchical cluster
gcc.tsheatmap: correlaiton and clustering analysis of tissue-specific genes
getsgene: identify tissue(or condtion)-specific genes
rsgcc.gui: graphical user interface (GUI) of rsgcc package
rsgcc-package: Gini methodology-based correlation and clustering analysis of...
See all...

All man pages Function index File listing

Man pages

adjacencymatrix: adjacency matrix calculation
cor.matrix: correlation calculation for a set of genes
cor.pair: compute the correlation between two genes
data: example of RNA-Seq gene expression data
gcc.corfinal: get the final correlaiton and p-value of Gini method
gcc.dist: compute distance matrix for hierarchical clustering
gcc.hclust: hierarchical cluster
gcc.heatmap: heat map
gcc.tsheatmap: correlaiton and clustering analysis of tissue-specific genes
getsgene: identify tissue(or condtion)-specific genes
onegcc: compute one Gini correlation coefficient
rsgcc.gui: graphical user interface (GUI) of rsgcc package
rsgcc-package: Gini methodology-based correlation and clustering analysis of...
uniqueTissues: get tissue information

Functions

Files

MD5
src
src/points.h
src/points.c
src/mi.h
src/mi.c
src/iqsort.h
src/grid.h
src/grid.c
src/bridge.c
src/Makevars.win
src/Makevars
man
man/uniqueTissues.Rd
man/rsgcc.gui.Rd
man/rsgcc-package.Rd
man/onegcc.Rd
man/getsgene.Rd
man/gcc.tsheatmap.Rd
man/gcc.heatmap.Rd
man/gcc.hclust.Rd
man/gcc.dist.Rd
man/gcc.corfinal.Rd
man/data.Rd
man/cor.pair.Rd
man/cor.matrix.Rd
man/adjacencymatrix.Rd
data
data/rsgcc.rda
data/datalist
R
R/tsheatmap.R
R/tsgene.R
R/rsgccgui.R
R/rsgcc.R
R/gethclust.R
R/getdist.R
NAMESPACE
DESCRIPTION
rsgcc documentation built on May 19, 2017, 10:27 p.m.

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