Package: enveomics.R 1.9.1

enveomics.R: Various Utilities for Microbial Genomics and Metagenomics

A collection of functions for microbial ecology and other applications of genomics and metagenomics. Companion package for the Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016 <doi:10.7287/peerj.preprints.1900v1>).

Authors:Luis M. Rodriguez-R [aut, cre]

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enveomics.R.pdf |enveomics.R.html✨
enveomics.R/json (API)

# Install 'enveomics.R' in R:
install.packages('enveomics.R', repos = c('https://lmrodriguezr.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • growth.curves - Bacterial growth curves for three Escherichia coli mutants
  • phyla.counts - Counts of microbial phyla in four sites

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

35 exports 0.09 score 14 dependencies 26 scripts 504 downloads

Last updated 8 months agofrom:50e0516c80. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 28 2024
R-4.5-winOKAug 28 2024
R-4.5-linuxOKAug 28 2024
R-4.4-winOKAug 28 2024
R-4.4-macOKAug 28 2024
R-4.3-winOKAug 28 2024
R-4.3-macOKAug 28 2024

Exports:enve.barplotenve.clioptsenve.col.alphaenve.col2alphaenve.df2distenve.df2dist.groupenve.df2dist.listenve.growthcurveenve.prefscoreenve.prune.distenve.recplotenve.recplot2enve.recplot2.ANIrenve.recplot2.changeCutoffenve.recplot2.compareIdentitiesenve.recplot2.coordinatesenve.recplot2.corePeakenve.recplot2.extractWindowsenve.recplot2.findPeaksenve.recplot2.findPeaks.emenve.recplot2.findPeaks.emautoenve.recplot2.findPeaks.mowerenve.recplot2.seqdepthenve.recplot2.windowDepthThresholdenve.selvectorenve.tribsenve.tribs.testenve.truncateplot.enve.GrowthCurveplot.enve.RecPlot2plot.enve.TRIBSplot.enve.TRIBStestsummary.enve.GrowthCurvesummary.enve.TRIBSsummary.enve.TRIBStest

Dependencies:fitdistrplusinvestrlatticeMASSMatrixMatrixModelsmnormtnlmenumDerivquantregrlangsnSparseMsurvival

Readme and manuals

Help Manual

Help pageTopics
Attribute accessor$,enve.GrowthCurve-method
Attribute accessor$,enve.RecPlot2-method
Attribute accessor$,enve.RecPlot2.Peak-method
Enveomics: Prune Iter (Internal Function)enve.__prune.iter
Enveomics: Prune Reduce (Internal Function)enve.__prune.reduce
Enveomics: TRIBS - Internal Ancillary Functionenve.__tribs
Enveomics: Barplotenve.barplot
Enveomics: Clioptsenve.cliopts
Enveomics: Color Alphaenve.col.alpha
Enveomics: Color to Alpha (deprecated)enve.col2alpha
Enveomics: Data Frame to Distenve.df2dist
Enveomics: Data Frame to Dist (Group)enve.df2dist.group
Enveomics: Data Frame to Dist (List)enve.df2dist.list
Enveomics: Growth Curveenve.growthcurve
Enveomics: Growth Curve S4 Classenve.GrowthCurve enve.GrowthCurve-class
Enveomics: Pref Scoreenve.prefscore
Enveomics: Prune Distenve.prune.dist
Enveomics: Recruitment Plotsenve.recplot
Enveomics: Recruitment Plot (2)enve.recplot2
Enveomics: Recruitment Plot (2) - S4 Classenve.RecPlot2 enve.RecPlot2-class
Enveomics: Recruitment Plot (2) Internal Ancillary Functionenve.recplot2.__counts
Enveomics: Recruitment Plot (2) Peak S4 Class - Internal Ancillary Functionenve.recplot2.__peakHist
Enveomics: Recruitment Plot (2) Peak Finder - Internal Ancillary Functionenve.recplot2.__whichClosestPeak
Enveomics: Recruitment Plot (2) ANI Estimateenve.recplot2.ANIr
Enveomics: Recruitment Plot (2) Change Cutoffenve.recplot2.changeCutoff
Enveomics: Recruitment Plot (2) Compare Identitiesenve.recplot2.compareIdentities
Enveomics: Recruitment Plot (2) Coordinatesenve.recplot2.coordinates
Enveomics: Recruitment Plot (2) Core Peak Finderenve.recplot2.corePeak
Enveomics: Recruitment Plot (2) Extract Windowsenve.recplot2.extractWindows
Enveomics: Recruitment Plot (2) Peak Finderenve.recplot2.findPeaks
Enveomics: Recruitment Plot (2) EM Peak Finder - Internal Ancillary Function Expectationenve.recplot2.findPeaks.__em_e
Enveomics: Recruitment Plot (2) Em Peak Finder - Internal Ancillary Function Maximizationenve.recplot2.findPeaks.__em_m
Enveomics: Recruitment Plot (2) EMauto Peak Finder - Internal Ancillary Functionenve.recplot2.findPeaks.__emauto_one
Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 1enve.recplot2.findPeaks.__mow_one
Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 2enve.recplot2.findPeaks.__mower
Enveomics: Recruitment Plot (2) Em Peak Finderenve.recplot2.findPeaks.em
Enveomics: Recruitment Plot (2) Emauto Peak Finderenve.recplot2.findPeaks.emauto
Enveomics: Recruitment Plot (2) Mowing Peak Finderenve.recplot2.findPeaks.mower
Enveomics: Recruitment Plot (2) Peak - S4 Classenve.RecPlot2.Peak enve.RecPlot2.Peak-class
Enveomics: Recruitment Plot (2) Sequencing Depthenve.recplot2.seqdepth
Enveomics: Recruitment Plot (2) Window Depth Thresholdenve.recplot2.windowDepthThreshold
Enveomics: Selection vectorenve.selvector
Enveomics: TRIBSenve.tribs
Enveomics: TRIBS S4 Classenve.TRIBS enve.TRIBS-class
Enveomics: TRIBS Mergeenve.TRIBS.merge
Enveomics: TRIBS Testenve.tribs.test
Enveomics: TRIBS Test S4 Classenve.TRIBStest enve.TRIBStest-class
Enveomics: Truncateenve.truncate
Bacterial growth curves for three Escherichia coli mutantsgrowth.curves
Counts of microbial phyla in four sitesphyla.counts
Enveomics: Plot of Growth Curveplot.enve.GrowthCurve
Enveomics: Recruitment Plot (2)plot.enve.RecPlot2
Enveomics: TRIBS Plotplot.enve.TRIBS
Enveomics: TRIBS Plot Testplot.enve.TRIBStest
Enveomics: Summary of Growth Curvesummary.enve.GrowthCurve
Enveomics: TRIBS Summarysummary.enve.TRIBS
Enveomics: TRIBS Summary Testsummary.enve.TRIBStest