Package: TcGSA 0.12.13

Boris P Hejblum

TcGSA: Time-Course Gene Set Analysis

Implementation of Time-course Gene Set Analysis (TcGSA), a method for analyzing longitudinal gene-expression data at the gene set level. Method is detailed in: Hejblum, Skinner & Thiebaut (2015) <doi:10.1371/journal.pcbi.1004310>.

Authors:Boris P Hejblum [aut, cre], Damien Chimits [aut], Anthony Devaux [aut]

TcGSA_0.12.13.tar.gz
TcGSA_0.12.13.zip(r-4.7)TcGSA_0.12.13.zip(r-4.6)TcGSA_0.12.13.zip(r-4.5)
TcGSA_0.12.13.tgz(r-4.6-any)TcGSA_0.12.13.tgz(r-4.5-any)
TcGSA_0.12.13.tar.gz(r-4.7-any)TcGSA_0.12.13.tar.gz(r-4.6-any)
TcGSA_0.12.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TcGSA/json (API)

# Install 'TcGSA' in R:

install.packages('TcGSA', repos = c('https://sistm.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sistm/tcgsa/issues

Pkgdown/docs site:https://sistm.github.io

Datasets:

design - Simulated Data for TcGSA
expr_1grp - Simulated Data for TcGSA
expr_2grp - Simulated Data for TcGSA
gmt_sim - Simulated Data for TcGSA

On CRAN:

5.38 score 6 stars 372 downloads 4 mentions 15 exports 44 dependencies

Last updated from:0c8885d121. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	194
source / vignettes	OK	515
linux-release-x86_64	OK	194
macos-release-arm64	OK	150
macos-oldrel-arm64	OK	113
windows-devel	OK	142
windows-release	OK	122
windows-oldrel	OK	138
wasm-release	OK	141

Exports:clustTrend dchisqmix multtest.TcGSA pchisqmix plot1GS plotFit.GS plotMultipleGS plotPat.1GS plotPat.TcGSA plotSelect.GS qchisqmix rchisqmix signifLRT.TcGSA TcGSA.LR TcGSA.LR.parallel

Dependencies:Biobase BiocGenerics boot cli cluster cowplot cpp11 farver generics ggplot2 glue GSA gtable gtools isoband labeling lattice lifecycle lme4 magrittr MASS Matrix minqa multtest nlme nloptr plyr R6 rbibutils RColorBrewer Rcpp RcppEigen Rdpack reformulas reshape2 rlang S7 scales stringi stringr survival vctrs viridisLite withr

User guide to the TcGSA R package

Rendered fromTcGSA_userguide.Rmdusingknitr::rmarkdown

Last update: 2025-07-22
Started: 2017-07-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Time-course Gene Set Analysis	TcGSA-package TcGSA
Cluster the genes dynamics into different dominant trends.	ClusteredTrends clustTrend plot.ClusteredTrends print.ClusteredTrends
Simulated Data for TcGSA	data_simu_TcGSA design expr_1grp expr_2grp gmt_sim
Computing the P-value of the Likelihood Ratios Applying a Multiple Testing Correction	multtest.TcGSA
Plot a Gene Set Trends Heatmap.	plot.TcGSA
Plotting a Specific Gene Set	plot1GS
Plotting function for exploring the fitness of the mixed modeling used in TcGSA	plotFit.GS
Plotting Multiple Gene Sets in a single plot	plotMultipleGS
Plotting a Specific Gene Set Stratifying on Patients	plotPat.1GS
Plot a Gene Set Trends Heatmap for each Patient.	plotPat.TcGSA
Plotting (several) Selected Gene Set(s) in some Subjects	plotSelect.GS
Chi-Squared Mixtures Distribution	chisqmix dchisqmix pchisqmix qchisqmix rchisqmix
Identifying the Significant Gene Sets	signifLRT.TcGSA
Summarizing TcGSA	print.summary.TcGSA summary.TcGSA
Computing the Likelihood Ratios for the Gene Sets under Scrutiny	print.TcGSA print.TcGSA.LR TcGSA.LR
Parallel computing the Likelihood Ratios for the Gene Sets under Scrutiny	TcGSA.LR.parallel