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TcGSA (version 0.10.5)

Time-Course Gene Set Analysis

Description

Implementation of Time-course Gene Set Analysis(TcGSA), a method for analyzing longitudinal gene-expression data at the gene set level.

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Version

Install

install.packages('TcGSA')

Monthly Downloads

327

Version

0.10.5

License

GPL-2 | file LICENSE

Maintainer

Boris P. Hejblum

Last Published

May 3rd, 2017

Functions in TcGSA (0.10.5)

TcGSA-internal

Internal TcGSA Functions

TcGSA-package

Time-course Gene Set Analysis

TcGSA.LR

Computing the Likelihood Ratios for the Gene Sets under Scrutiny

TcGSA.LR.parallel

Parallel computing the Likelihood Ratios for the Gene Sets under Scrutiny

plot1GS

Plotting a Specific Gene Set

plotFit.GS

Plotting function for exploring the fittness of the mixed modeling used in TcGSA

multtest.TcGSA

Computing the P-value of the Likelihood Ratios Applying a Multiple Testing Correction

plot.TcGSA

Plot a Gene Set Trends Heatmap.

clustTrend

Cluster the genes dynamics into different dominant trends.

data_simu_TcGSA

Simulated Data for TcGSA

summary.TcGSA

Summarizing TcGSA

rmixchisq

Random Generation of Chi-square Mixtures

plotSelect.GS

Plotting (several) Selected Gene Set(s) in some Subjects

pval_simu

Computing P-values with a Simulated Sample from the Null Distribution

signifLRT.TcGSA

Identifiying the Significant Gene Sets

plotPat.TcGSA

Plot a Gene Set Trends Heatmap for each Patient.

plotPat.1GS

Plotting a Specific Gene Set Stratifying on Patients