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

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).

Author
Chuang Ma, Xiangfeng Wang
Date of publication
2013-06-18 07:40:43
Maintainer
Chuang Ma <chuangma2006@gmail.com>
License
GPL (>= 2)
Version
1.0.6
URLs

View on CRAN

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

Files in this package

rsgcc
rsgcc/MD5
rsgcc/src
rsgcc/src/points.h
rsgcc/src/points.c
rsgcc/src/mi.h
rsgcc/src/mi.c
rsgcc/src/iqsort.h
rsgcc/src/grid.h
rsgcc/src/grid.c
rsgcc/src/bridge.c
rsgcc/src/Makevars.win
rsgcc/src/Makevars
rsgcc/man
rsgcc/man/uniqueTissues.Rd
rsgcc/man/rsgcc.gui.Rd
rsgcc/man/rsgcc-package.Rd
rsgcc/man/onegcc.Rd
rsgcc/man/getsgene.Rd
rsgcc/man/gcc.tsheatmap.Rd
rsgcc/man/gcc.heatmap.Rd
rsgcc/man/gcc.hclust.Rd
rsgcc/man/gcc.dist.Rd
rsgcc/man/gcc.corfinal.Rd
rsgcc/man/data.Rd
rsgcc/man/cor.pair.Rd
rsgcc/man/cor.matrix.Rd
rsgcc/man/adjacencymatrix.Rd
rsgcc/data
rsgcc/data/rsgcc.rda
rsgcc/data/datalist
rsgcc/R
rsgcc/R/tsheatmap.R
rsgcc/R/tsgene.R
rsgcc/R/rsgccgui.R
rsgcc/R/rsgcc.R
rsgcc/R/gethclust.R
rsgcc/R/getdist.R
rsgcc/NAMESPACE
rsgcc/DESCRIPTION