Package: TMixClust 1.29.0
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:
TMixClust_1.29.0.tar.gz
TMixClust_1.29.0.zip(r-4.5)TMixClust_1.29.0.zip(r-4.4)TMixClust_1.29.0.zip(r-4.3)
TMixClust_1.29.0.tgz(r-4.4-any)TMixClust_1.29.0.tgz(r-4.3-any)
TMixClust_1.29.0.tar.gz(r-4.5-noble)TMixClust_1.29.0.tar.gz(r-4.4-noble)
TMixClust_1.29.0.tgz(r-4.4-emscripten)TMixClust_1.29.0.tgz(r-4.3-emscripten)
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')) |
- 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-1.29.0(bioc 3.21)TMixClust-1.28.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwarestatisticalmethodclusteringtimecoursegeneexpression
Last updated 2 months agofrom:67da9fc4e5. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | OK | Nov 30 2024 |
| R-4.5-linux | OK | Nov 30 2024 |
| R-4.4-win | OK | Nov 30 2024 |
| R-4.4-mac | OK | Nov 30 2024 |
| R-4.3-win | OK | Nov 30 2024 |
| R-4.3-mac | OK | Nov 30 2024 |
Exports:analyse_stabilitygenerate_TMixClust_reportget_time_series_dfget_time_series_df_bioplot_silhouetteplot_time_series_dfTMixClust
Dependencies:BHBiobaseBiocGenericsBiocParallelclassclustercodetoolscpp11flexclustformatRfutile.loggerfutile.optionsgenericsgsslambda.rlatticeMASSmodeltoolsmvtnormRsolnpsnowSPEMtruncnormzoo
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 |
