Various Utilities for Microbial Genomics and Metagenomics
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Documentation for package ‘enveomics.R’ version 1.10.0
Help Pages
| $-method | Attribute accessor |
| $-method | Attribute accessor |
| $-method | Attribute accessor |
| enve.barplot | Enveomics: Barplot |
| enve.cliopts | Enveomics: Cliopts |
| enve.col.alpha | Enveomics: Color Alpha |
| enve.col2alpha | Enveomics: Color to Alpha (deprecated) |
| enve.df2dist | Enveomics: Data Frame to Dist |
| enve.df2dist.group | Enveomics: Data Frame to Dist (Group) |
| enve.df2dist.list | Enveomics: Data Frame to Dist (List) |
| enve.GrowthCurve | Enveomics: Growth Curve S4 Class |
| enve.growthcurve | Enveomics: Growth Curve |
| enve.GrowthCurve-class | Enveomics: Growth Curve S4 Class |
| enve.prefscore | Enveomics: Pref Score |
| enve.prune.dist | Enveomics: Prune Dist |
| enve.recplot | Enveomics: Recruitment Plots |
| enve.RecPlot2 | Enveomics: Recruitment Plot (2) - S4 Class |
| enve.recplot2 | Enveomics: Recruitment Plot (2) |
| enve.RecPlot2-class | Enveomics: Recruitment Plot (2) - S4 Class |
| enve.recplot2.ANIr | Enveomics: Recruitment Plot (2) ANI Estimate |
| enve.recplot2.changeCutoff | Enveomics: Recruitment Plot (2) Change Cutoff |
| enve.recplot2.compareIdentities | Enveomics: Recruitment Plot (2) Compare Identities |
| enve.recplot2.coordinates | Enveomics: Recruitment Plot (2) Coordinates |
| enve.recplot2.corePeak | Enveomics: Recruitment Plot (2) Core Peak Finder |
| enve.recplot2.extractWindows | Enveomics: Recruitment Plot (2) Extract Windows |
| enve.recplot2.findPeaks | Enveomics: Recruitment Plot (2) Peak Finder |
| enve.recplot2.findPeaks.em | Enveomics: Recruitment Plot (2) Em Peak Finder |
| enve.recplot2.findPeaks.emauto | Enveomics: Recruitment Plot (2) Emauto Peak Finder |
| enve.recplot2.findPeaks.mower | Enveomics: Recruitment Plot (2) Mowing Peak Finder |
| enve.recplot2.findPeaks.__emauto_one | Enveomics: Recruitment Plot (2) EMauto Peak Finder - Internal Ancillary Function |
| enve.recplot2.findPeaks.__em_e | Enveomics: Recruitment Plot (2) EM Peak Finder - Internal Ancillary Function Expectation |
| enve.recplot2.findPeaks.__em_m | Enveomics: Recruitment Plot (2) Em Peak Finder - Internal Ancillary Function Maximization |
| enve.recplot2.findPeaks.__mower | Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 2 |
| enve.recplot2.findPeaks.__mow_one | Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 1 |
| enve.RecPlot2.Peak | Enveomics: Recruitment Plot (2) Peak - S4 Class |
| enve.RecPlot2.Peak-class | Enveomics: Recruitment Plot (2) Peak - S4 Class |
| enve.recplot2.seqdepth | Enveomics: Recruitment Plot (2) Sequencing Depth |
| enve.recplot2.windowDepthThreshold | Enveomics: Recruitment Plot (2) Window Depth Threshold |
| enve.recplot2.__counts | Enveomics: Recruitment Plot (2) Internal Ancillary Function |
| enve.recplot2.__peakHist | Enveomics: Recruitment Plot (2) Peak S4 Class - Internal Ancillary Function |
| enve.recplot2.__whichClosestPeak | Enveomics: Recruitment Plot (2) Peak Finder - Internal Ancillary Function |
| enve.selvector | Enveomics: Selection vector |
| enve.TRIBS | Enveomics: TRIBS S4 Class |
| enve.tribs | Enveomics: TRIBS |
| enve.TRIBS-class | Enveomics: TRIBS S4 Class |
| enve.TRIBS.merge | Enveomics: TRIBS Merge |
| enve.tribs.test | Enveomics: TRIBS Test |
| enve.TRIBStest | Enveomics: TRIBS Test S4 Class |
| enve.TRIBStest-class | Enveomics: TRIBS Test S4 Class |
| enve.truncate | Enveomics: Truncate |
| enve.__prune.iter | Enveomics: Prune Iter (Internal Function) |
| enve.__prune.reduce | Enveomics: Prune Reduce (Internal Function) |
| enve.__tribs | Enveomics: TRIBS - Internal Ancillary Function |
| growth.curves | Bacterial growth curves for three Escherichia coli mutants |
| phyla.counts | Counts of microbial phyla in four sites |
| plot.enve.GrowthCurve | Enveomics: Plot of Growth Curve |
| plot.enve.RecPlot2 | Enveomics: Recruitment Plot (2) |
| plot.enve.TRIBS | Enveomics: TRIBS Plot |
| plot.enve.TRIBStest | Enveomics: TRIBS Plot Test |
| summary.enve.GrowthCurve | Enveomics: Summary of Growth Curve |
| summary.enve.TRIBS | Enveomics: TRIBS Summary |
| summary.enve.TRIBStest | Enveomics: TRIBS Summary Test |