Package: ClueR 1.4.2
ClueR: Cluster Evaluation
CLUster Evaluation (CLUE) is a computational method for identifying optimal number of clusters in a given time-course dataset clustered by cmeans or kmeans algorithms and subsequently identify key kinases or pathways from each cluster. Its implementation in R is called ClueR. See README on <https://github.com/PYangLab/ClueR> for more details. P Yang et al. (2015) <doi:10.1371/journal.pcbi.1004403>.
Authors:
ClueR_1.4.2.tar.gz
ClueR_1.4.2.zip(r-4.5)ClueR_1.4.2.zip(r-4.4)ClueR_1.4.2.zip(r-4.3)
ClueR_1.4.2.tgz(r-4.4-any)ClueR_1.4.2.tgz(r-4.3-any)
ClueR_1.4.2.tar.gz(r-4.5-noble)ClueR_1.4.2.tar.gz(r-4.4-noble)
ClueR_1.4.2.tgz(r-4.4-emscripten)ClueR_1.4.2.tgz(r-4.3-emscripten)
ClueR.pdf |ClueR.html✨
ClueR/json (API)
| # Install 'ClueR' in R: |
| install.packages('ClueR', repos = c('https://pyanglab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pyanglab/cluer/issues
- Pathways.DAVID - DAVID pathway annotations
- Pathways.KEGG - KEGG pathway annotations
- Pathways.biocarta - Biocarta pathway annotations
- Pathways.reactome - Reactome pathway annotations
- PhosphoELM.human - Phospho.ELM annotations for human
- PhosphoELM.mouse - Phospho.ELM annotations for mouse
- PhosphoSite.human - PhosphoSitePlus annotations for human
- PhosphoSite.mouse - PhosphoSitePlus annotations for mouse
- adipocyte - Mouse adipocyte differentiation gene expression (microarray) data
- hES - Human embryonic stem cell phosphoproteomics data
Last updated 1 years agofrom:6dbfcaa079. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 11 2024 |
| R-4.5-win | OK | Nov 11 2024 |
| R-4.5-linux | OK | Nov 11 2024 |
| R-4.4-win | OK | Nov 11 2024 |
| R-4.4-mac | OK | Nov 11 2024 |
| R-4.3-win | OK | Nov 11 2024 |
| R-4.3-mac | OK | Nov 11 2024 |
Exports:clustEnrichmentclustOptimalenrichmentTestfuzzPlotrunCluetemporalSimu
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CLUster Evaluation R package | ClueR-package CLUE ClueR |
| Mouse adipocyte differentiation gene expression (microarray) data | adipocyte |
| Cluster enrichment test | clustEnrichment |
| Generate optimal clustering | clustOptimal |
| Fisher's exact test-based enrichment test | enrichmentTest |
| Visualize fuzzy clustering results | fuzzPlot |
| Human embryonic stem cell phosphoproteomics data | hES |
| Biocarta pathway annotations | Pathways.biocarta |
| DAVID pathway annotations | Pathways.DAVID |
| KEGG pathway annotations | Pathways.KEGG |
| Reactome pathway annotations | Pathways.reactome |
| Phospho.ELM annotations for human | PhosphoELM.human |
| Phospho.ELM annotations for mouse | PhosphoELM.mouse |
| PhosphoSitePlus annotations for human | PhosphoSite.human |
| PhosphoSitePlus annotations for mouse | PhosphoSite.mouse |
| Run CLUster Evaluation | runClue |
| Temporal data simulation | temporalSimu |
