Package: KOGMWU 1.2
KOGMWU: Functional Summary and Meta-Analysis of Gene Expression Data
Rank-based tests for enrichment of KOG (euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a continuous measure. The meta-analysis is based on correlation of KOG delta-ranks across datasets (delta-rank is the difference between mean rank of genes belonging to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to indicate significant and non-significant genes), one-tailed Fisher's exact test for over-representation of each KOG class among significant genes will be performed.
Authors:
KOGMWU_1.2.tar.gz
KOGMWU_1.2.zip(r-4.5)KOGMWU_1.2.zip(r-4.4)KOGMWU_1.2.zip(r-4.3)
KOGMWU_1.2.tgz(r-4.4-any)KOGMWU_1.2.tgz(r-4.3-any)
KOGMWU_1.2.tar.gz(r-4.5-noble)KOGMWU_1.2.tar.gz(r-4.4-noble)
KOGMWU_1.2.tgz(r-4.4-emscripten)KOGMWU_1.2.tgz(r-4.3-emscripten)
KOGMWU.pdf |KOGMWU.html✨
KOGMWU/json (API)
| # Install 'KOGMWU' in R: |
| install.packages('KOGMWU', repos = c('https://z0on.r-universe.dev', 'https://cloud.r-project.org')) |
- adults.3dHeat.logFoldChange - Heat stress response of adult coral
- gene2kog - KOG class annotations
- larvae.longTerm - Long-term heat stress response of coral larvae
- larvae.shortTerm - Short-term heat stress response of coral larvae
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 years agofrom:6ac264c08e. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 31 2024 |
| R-4.5-win | OK | Aug 31 2024 |
| R-4.5-linux | OK | Aug 31 2024 |
| R-4.4-win | OK | Aug 31 2024 |
| R-4.4-mac | OK | Aug 31 2024 |
| R-4.3-win | OK | Aug 31 2024 |
| R-4.3-mac | OK | Aug 31 2024 |
Exports:corrPlotkog.ftkog.mwukog.mwutmakeDeltaRanksTablepanel.corpanel.cor.pval
Dependencies:clicolorspacefarvergluegtablelabelinglifecyclemunsellpheatmapR6RColorBrewerrlangscalesviridisLite
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Functional summary and meta-analysis of gene expression data | KOGMWU-package KOGMWU |
| Heat stress response of adult coral | adults.3dHeat.logFoldChange |
| Plots a pairwise correlation with linear regression line | corrPlot |
| KOG class annotations | gene2kog |
| One-tailed Fisher's exact test for KOG enrichment. | kog.ft |
| Tests for KOG class enrichment. | kog.mwu |
| Mann-Whitney U test for KOG enrichment. | kog.mwut |
| Long-term heat stress response of coral larvae | larvae.longTerm |
| Short-term heat stress response of coral larvae | larvae.shortTerm |
| Make a combined delta-ranks table from several kog.mwu() results. | makeDeltaRanksTable |
| accessory function for pairs() to display Pearson correlations | panel.cor |
| accessory function for pairs() to display pvalue of the Pearson correlation | panel.cor.pval |
