R: Various Utilities for Microbial Genomics and Metagenomics

# Various Utilities for Microbial Genomics and Metagenomics

## Documentation for package ‘enveomics.R’ version 1.10.0

- DESCRIPTION file.

## 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