Package: TMixClust 1.27.0

Monica Golumbeanu

TMixClust: Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets.

Authors:Monica Golumbeanu <[email protected]>

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TMixClust.pdf |TMixClust.html✨
TMixClust/json (API)
NEWS

# Install 'TMixClust' in R:

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

Datasets:

best_clust_toy_obj - TMixClust object containing the optimal clustering solution for the toy data with 3 clusters.
best_clust_yeast_obj - TMixClust object containing the optimal clustering solution for the yeast data.
toy_data_df - Simulated time-series gene expression data

On BioConductor:TMixClust-1.27.0(bioc 3.20)TMixClust-1.26.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

7 exports 0.71 score 23 dependencies 2 mentions

Last updated 2 months agofrom:41dbf6657b

Exports:analyse_stability generate_TMixClust_report get_time_series_df get_time_series_df_bio plot_silhouette plot_time_series_df TMixClust

Dependencies:BH Biobase BiocGenerics BiocParallel class cluster codetools cpp11 flexclust formatR futile.logger futile.options gss lambda.r lattice MASS modeltools mvtnorm Rsolnp snow SPEM truncnorm zoo

Clustering time series gene expression data with TMixClust

Rendered fromTMixClust.Rnwusingknitr::knitron Jun 30 2024.

Last update: 2018-02-01
Started: 2017-07-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The main usages of TMixClust	TMixClust-package
Stability analysis, clustering evaluation and optimal solution selection	analyse_stability
TMixClust object containing the optimal clustering solution for the toy data with 3 clusters.	best_clust_toy_obj
TMixClust object containing the optimal clustering solution for the yeast data.	best_clust_yeast_obj
Generates a series of files containing a summary of the TMixClust analysis results	generate_TMixClust_report
Extracts a time series data frame from a text file	get_time_series_df
Extracts a time series data frame from a Bioconductor Biobase ExpressionSet object.	get_time_series_df_bio
Generates a silhouette plot for a given clustering configuration.	plot_silhouette
Plots all the time series stored in a data frame object	plot_time_series_df
Clusters the time series data in a given number of groups	TMixClust
Simulated time-series gene expression data	toy_data_df