TcGSA: Time-Course Gene Set Analysis

Implementation of TcGSA, a method for analyzing longitudinal gene-expression data at the gene set level.

Author
Boris P. Hejblum [aut, cre], Damien Chimits [aut]
Date of publication
2015-12-22 18:12:44
Maintainer
Boris P. Hejblum <bhejblum@hsph.harvard.edu>
License
GPL-2 | file LICENSE
Version
0.10.1

View on CRAN

Man pages

clustTrend
Cluster the genes dynamics into different dominant trends.
data_simu_TcGSA
Simulated Data for TcGSA
multtest.TcGSA
Computing the P-value of the Likelihood Ratios Applying a...
plot1GS
Plotting a Specific Gene Set
plotFit.GS
Plotting function for exploring the fittness of the mixed...
plotPat.1GS
Plotting a Specific Gene Set Stratifying on Patients
plotPat.TcGSA
Plot a Gene Set Trends Heatmap for each Patient.
plotSelect.GS
Plotting (several) Selected Gene Set(s) in some Subjects
plot.TcGSA
Plot a Gene Set Trends Heatmap.
pval_simu
Computing P-values with a Simulated Sample from the Null...
rmixchisq
Random Generation of Chi-square Mixtures
signifLRT.TcGSA
Identifiying the Significant Gene Sets
summary.TcGSA
Summarizing TcGSA
TcGSA-internal
Internal TcGSA Functions
TcGSA.LR
Computing the Likelihood Ratios for the Gene Sets under...
TcGSA.LR.parallel
Parallel computing the Likelihood Ratios for the Gene Sets...
TcGSA-package
Time-course Gene Set Analysis

Files in this package

TcGSA
TcGSA/inst
TcGSA/inst/CITATION
TcGSA/NAMESPACE
TcGSA/data
TcGSA/data/data_simu_TcGSA.RData
TcGSA/R
TcGSA/R/signifLRT.TcGSA.R
TcGSA/R/STSdist.R
TcGSA/R/TcGSA.dataLME.R
TcGSA/R/TcGSA.formula.R
TcGSA/R/plotPat.1GS.R
TcGSA/R/multtest.TcGSA.R
TcGSA/R/rmixchisq.R
TcGSA/R/plotSelect.GS.R
TcGSA/R/plotFit.GS.R
TcGSA/R/summary.TcGSA.R
TcGSA/R/MYheatmap.2.R
TcGSA/R/TcGSA-internal.R
TcGSA/R/pval_simu.R
TcGSA/R/clustTrend.R
TcGSA/R/TcGSA.LR.R
TcGSA/R/plot.TcGSA.R
TcGSA/R/plotPat.TcGSA.R
TcGSA/R/TcGSA.LR.parallel.R
TcGSA/R/TcGSA-package.R
TcGSA/R/plot1GS.R
TcGSA/MD5
TcGSA/README
TcGSA/DESCRIPTION
TcGSA/man
TcGSA/man/plot1GS.Rd
TcGSA/man/clustTrend.Rd
TcGSA/man/multtest.TcGSA.Rd
TcGSA/man/plotPat.1GS.Rd
TcGSA/man/signifLRT.TcGSA.Rd
TcGSA/man/plotPat.TcGSA.Rd
TcGSA/man/plotFit.GS.Rd
TcGSA/man/TcGSA.LR.parallel.Rd
TcGSA/man/data_simu_TcGSA.Rd
TcGSA/man/TcGSA-package.Rd
TcGSA/man/pval_simu.Rd
TcGSA/man/TcGSA.LR.Rd
TcGSA/man/summary.TcGSA.Rd
TcGSA/man/plotSelect.GS.Rd
TcGSA/man/plot.TcGSA.Rd
TcGSA/man/TcGSA-internal.Rd
TcGSA/man/rmixchisq.Rd
TcGSA/LICENSE