Package: EMMIXgene 0.1.4
Andrew Thomas Jones
EMMIXgene: A Mixture Model-Based Approach to the Clustering of Microarray Expression Data
Provides unsupervised selection and clustering of microarray data using mixture models. Following the methods described in McLachlan, Bean and Peel (2002) <doi:10.1093/bioinformatics/18.3.413> a subset of genes are selected based one the likelihood ratio statistic for the test of one versus two components when fitting mixtures of t-distributions to the expression data for each gene. The dimensionality of this gene subset is further reduced through the use of mixtures of factor analyzers, allowing the tissue samples to be clustered by fitting mixtures of normal distributions.
Authors:
EMMIXgene_0.1.4.tar.gz
EMMIXgene_0.1.4.tar.gz(r-4.5-noble)EMMIXgene_0.1.4.tar.gz(r-4.4-noble)
EMMIXgene_0.1.4.tgz(r-4.4-emscripten)EMMIXgene_0.1.4.tgz(r-4.3-emscripten)
EMMIXgene.pdf |EMMIXgene.html✨
EMMIXgene/json (API)
NEWS
| # Install 'EMMIXgene' in R: |
| install.packages('EMMIXgene', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- alon_data - Normalized gene expression values from Alon et al. (1999).
- golub_data - Normalized gene expression values from Golub et al. (1999).
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 9 months agofrom:1ac8dc5713. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 18 2024 |
| R-4.5-linux-x86_64 | OK | Oct 18 2024 |
Exports:all_cluster_tissuescluster_genescluster_tissuesheat_mapsplot_single_geneselect_genestop_genes_cluster_tissues
Dependencies:BHclicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmclustmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshaperlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clusters tissues using all group means | all_cluster_tissues |
| Normalized gene expression values from Alon et al. (1999). | alon_data |
| Clusters genes using mixtures of normal distributions | cluster_genes |
| Clusters tissues | cluster_tissues |
| EMMIXgene: | EMMIXgene |
| Normalized gene expression values from Golub et al. (1999). | golub_data |
| Heat maps | heat_maps |
| Plot a single gene expression histogram with best fitted mixture of t-distributions. | plot_single_gene |
| Selects genes using the EMMIXgene algorithm. | select_genes |
| Cluster tissues | top_genes_cluster_tissues |
