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 ).


Installing enveomics.R

To install the latest version of enveomics.R uploaded to CRAN, execute in R:

install.packages('enveomics.R')

To install the current developer version of enveomics.R, execute in R:

install.packages('devtools')
library('devtools')
install_github('lmrodriguezr/enveomics', subdir='enveomics.R')

Using enveomics.R

To load enveomics.R, simply execute:

library(enveomics.R);

And open help messages using any of the following commands:

?enveomics.R
?enve.barplot
?enve.recplot2
?enve.recplot2.compareIdentities
?enve.recplot2.changeCutoff
?enve.recplot2.findPeaks
?enve.recplot2.corePeak
?enve.recplot2.windowDepthThreshold
?enve.recplot2.extractWindows
?enve.recplot2.coordinates
?enve.recplot2.seqdepth
?enve.recplot2.ANIr
?enve.prune.dist
?enve.tribs
?enve.tribs.test
?enve.growthcurve
?enve.col.alpha
?enve.truncate

You can run some examples using these libraries in the enveomics-GUI.

For additional information on recruitment plots, see the Recruitment plots working document.

Changelog

  • 1.4.4: Removes modeest library as requirement, and replaces mower peak-finder initialization to median (instead of mode).
  • 1.4.2: Solved bug #36.
  • 1.4.0: New option pos.breaks.tsv for enve.recplot2.
  • 1.3.4: Gracefully handles and plots recruitment plots with insufficient data to find peaks.
  • 1.3.3: New function enve.recplot2.windowDepthThreshold.
  • 1.3.2: New option panel.fun for plot.enve.RecPlot2.
  • 1.3.1: New function enve.truncate.
  • 1.3: Several bug fixes and new utilities for recruitment plots (recplot2).
  • 1.1.0: New function enve.growthcurve and related class enve.GrowthCurve with S3 methods plot and summary.
  • 1.0.2: Fine-tuned default parameters in enve.recplot2.findPeaks and solved a minor bug in enve.recplot2 that caused failures in low-coverage datasets when using too many threads.
  • 1.0.1: enve.recplot2 now supports pos.breaks=0 to define a bin per subject sequence.

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("enveomics.R")

1.8.0 by Luis M. Rodriguez-R, a year ago


http://enve-omics.ce.gatech.edu/enveomics


Browse source code at https://github.com/cran/enveomics.R


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


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


Artistic-2.0 license


Depends on stats, methods, parallel, fitdistrplus, sn, investr

Suggests tools, vegan, ape, picante, gplots, optparse


See at CRAN