Introduction | Moderated Tests Based on Package limma | Moderated t-Test | Moderated 1-Way ANOVA | Pairwise moderated t-tests | Pairwise Comparisons | FC and logFC | Aggregating Technical Replicates | 1- and 2-Way ANOVA | Correlation Distance Matrix | MAD Matrix | Similarity Matrices | Colors for Heatmaps | String Alignment | String Distances | String Similarities | Optimal Alignment | sessionInfo | References
Package: MKomics 0.8
MKomics: Omics Data Analysis
Similarity plots based on correlation and median absolute deviation (MAD); adjusting colors for heatmaps; aggregate technical replicates; calculate pairwise fold-changes and log fold-changes; compute one- and two-way ANOVA; simplified interface to package 'limma' (Ritchie et al. (2015), <doi:10.1093/nar/gkv007> ) for moderated t-test and one-way ANOVA; Hamming and Levenshtein (edit) distance of strings as well as optimal alignment scores for global (Needleman-Wunsch) and local (Smith-Waterman) alignments with constant gap penalties (Merkl and Waack (2009), ISBN:978-3-527-32594-8).
Authors:
MKomics_0.8.tar.gz
MKomics_0.8.zip(r-4.7)MKomics_0.8.zip(r-4.6)MKomics_0.8.zip(r-4.5)
MKomics_0.8.tgz(r-4.6-any)MKomics_0.8.tgz(r-4.5-any)
MKomics_0.8.tar.gz(r-4.7-any)MKomics_0.8.tar.gz(r-4.6-any)
MKomics_0.8.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MKomics/json (API)
| # Install 'MKomics' in R: |
| install.packages('MKomics', repos = c('https://stamats.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stamats/mkomics/issues
Last updated from:799e9de1f4. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 161 | ||
| source / vignettes | OK | 223 | ||
| linux-release-x86_64 | OK | 150 | ||
| macos-release-arm64 | OK | 132 | ||
| macos-oldrel-arm64 | OK | 122 | ||
| windows-devel | OK | 108 | ||
| windows-release | OK | 107 | ||
| windows-oldrel | OK | 100 | ||
| wasm-release | OK | 121 |
Exports:corDistcorPlotcorPlot2heatmapColmadMatrixmadPlotmadPlot2mod.oneway.testmod.t.testoneWayAnovapairwise.fcpairwise.logfcpairwise.mod.t.testrepMeanssimPlotsimPlot2stringDiststringSimtraceBacktwoWayAnova
Dependencies:BiocGenericscirclizeclueclustercodetoolscolorspaceComplexHeatmapcrayonDEoptimRdigestdoParallelforeachgenericsGetoptLongGlobalOptionsIRangesiteratorslimmamatrixStatspngRColorBrewerrjsonrobustbaseS4Vectorsshapestatmod
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Omics Data Analysis. | MKomics-package MKomics |
| Correlation Distance Matrix Computation | corDist |
| Plot of similarity matrix based on correlation | corPlot corPlot2 |
| Generate colors for heatmaps | heatmapCol |
| Compute MAD between colums of a matrix or data.frame | madMatrix |
| Plot of similarity matrix based on MAD | madPlot madPlot2 |
| Moderated 1-Way ANOVA | mod.oneway.test |
| Moderated t-Test | mod.t.test |
| A function for Analysis of Variance | oneWayAnova |
| Compute pairwise fold changes | pairwise.fc |
| Compute pairwise log-fold changes | pairwise.logfc |
| Pairwise Moderated t-Tests | pairwise.mod.t.test |
| Compute mean of replicated spots | repMeans |
| Plot of a similarity matrix. | simPlot simPlot2 |
| Function to compute distances between strings | stringDist |
| Function to compute similarity scores between strings | stringSim |
| Function to trace back | traceBack |
| A function for Analysis of Variance | twoWayAnova |
