Package: Nonpareil 3.5.3

Nonpareil: Metagenome Coverage Estimation and Projections for 'Nonpareil'

Plot, process, and analyze NPO files produced by 'Nonpareil' <http://enve-omics.ce.gatech.edu/nonpareil/>.

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

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Nonpareil/json (API)

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

Peer review:

On CRAN:

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

2.53 score 34 scripts 359 downloads 33 mentions 19 exports 0 dependencies

Last updated 4 months agofrom:f0ee9d5563. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:Nonpareil.add.curveNonpareil.antifNonpareil.colNonpareil.coverage_factorNonpareil.curveNonpareil.curve.batchNonpareil.fNonpareil.fit_modelNonpareil.legendNonpareil.read_dataNonpareil.read_metadataNonpareil.setplot.Nonpareil.Curveplot.Nonpareil.Setpredict.Nonpareil.Curveprint.Nonpareil.Curveprint.Nonpareil.Setsummary.Nonpareil.Curvesummary.Nonpareil.Set

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Alias of 'Nonpareil.add.curve'.+,Nonpareil.Set,ANY-method
Get attribute.$,Nonpareil.Curve-method
Get attribute.$,Nonpareil.Set-method
Set attribute.$<-,Nonpareil.Curve-method
Set attribute.$<-,Nonpareil.Set-method
Nonpareil: Metagenome Coverage Estimation and Projections for 'Nonpareil'.Nonpareil-package Nonpareil
Adds a 'Nonpareil.Curve' to a 'Nonpareil.Set'.Nonpareil.add.curve
Complement function of 'Nonpareil.f'.Nonpareil.antif
Returns the color of the curve.Nonpareil.col
Factor to transform redundancy into coverage (internal function).Nonpareil.coverage_factor
Generates a Nonpareil curve from an .npo fileNonpareil.curve
A single Nonpareil curve. This object can be produced by 'Nonpareil.curve' and supports S4 methods 'plot', 'summary', 'print', and 'predict'. For additional details, see help for 'summary.Nonpareil.Curve'.Nonpareil.Curve-class
Alias of 'Nonpareil.set'.Nonpareil.curve.batch
Function of the projected model.Nonpareil.f
Fit the sigmoidal model to the rarefied coverage.Nonpareil.fit_model
Generates a legend for Nonpareil plots.Nonpareil.legend
Read the data tables and extract direct estimates.Nonpareil.read_data
Read the metadata headers.Nonpareil.read_metadata
Generates a collection of Nonpareil curves (a 'Nonpareil.Set' object) and (optionally) plots all of them in a single canvas.Nonpareil.set
Collection of 'Nonpareil.Curve' objects. This object can be produced by 'Nonpareil.curve.batch' and supports S4 methods 'plot', 'summary', and 'print'.Nonpareil.Set-class
Plot a 'Nonpareil.Curve' object.plot.Nonpareil.Curve
Plot a 'Nonpareil.Set' object.plot.Nonpareil.Set
Predict the coverage for a given sequencing effort.predict.Nonpareil.Curve
Prints and returns invisibly a summary of the 'Nonpareil.Curve' results.print.Nonpareil.Curve
Prints and returns invisibly a summary of the 'Nonpareil.Set' results.print.Nonpareil.Set
Returns a summary of the 'Nonpareil.Curve' results.summary.Nonpareil.Curve
Returns a summary of the 'Nonpareil.Set' results.summary.Nonpareil.Set