Package: TRAMPR 1.0-10

TRAMPR: 'TRFLP' Analysis and Matching Package for R

Matching terminal restriction fragment length polymorphism ('TRFLP') profiles between unknown samples and a database of known samples. 'TRAMPR' facilitates analysis of many unknown profiles at once, and provides tools for working directly with electrophoresis output through to generating summaries suitable for community analyses with R's rich set of statistical functions. 'TRAMPR' also resolves the issues of multiple 'TRFLP' profiles within a species, and shared 'TRFLP' profiles across species.

Authors:Rich FitzJohn [aut, cre], Ian Dickie [aut]

TRAMPR_1.0-10.tar.gz
TRAMPR_1.0-10.zip(r-4.5)TRAMPR_1.0-10.zip(r-4.4)TRAMPR_1.0-10.zip(r-4.3)
TRAMPR_1.0-10.tgz(r-4.4-any)TRAMPR_1.0-10.tgz(r-4.3-any)
TRAMPR_1.0-10.tar.gz(r-4.5-noble)TRAMPR_1.0-10.tar.gz(r-4.4-noble)
TRAMPR_1.0-10.tgz(r-4.4-emscripten)TRAMPR_1.0-10.tgz(r-4.3-emscripten)
TRAMPR.pdf |TRAMPR.html✨
TRAMPR/json (API)

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

Peer review:

Bug tracker:https://github.com/richfitz/trampr/issues

Datasets:

On CRAN:

4.66 score 23 scripts 469 downloads 4 mentions 39 exports 0 dependencies

Last updated 3 years agofrom:0b0ec87e7b. Checks:7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 14 2025
R-4.5-winOKJan 14 2025
R-4.5-linuxOKJan 14 2025
R-4.4-winOKJan 14 2025
R-4.4-macOKJan 14 2025
R-4.3-winOKJan 14 2025
R-4.3-macOKJan 14 2025

Exports:[.TRAMPknowns[.TRAMPsamplesabsolute.minadd.knownadd.known.TRAMPadd.known.TRAMPknownsbuild.knownsclassifycombinecombine.TRAMPcombine.TRAMPknownscombine.TRAMPsamplescreate.diffsmatrixgroup.knownsgroup.knowns.TRAMPgroup.knowns.TRAMPknownslabels.TRAMPknownslabels.TRAMPsamplesload.abiload.abi.create.infoload.abi.create.templateplot.TRAMPplot.TRAMPknownsread.abiread.TRAMPknownsread.TRAMPsamplesrebuild.TRAMPremove.TRAMP.matchsummary.TRAMPsummary.TRAMPknownssummary.TRAMPsamplesTRAMPTRAMP.plotoneTRAMPknownsTRAMPsamplesTRAMPsamples.plotoneupdate.TRAMPwrite.TRAMPknownswrite.TRAMPsamples

Dependencies:

Introduction to TRAMPR

Rendered fromTRAMPRdemo.Rnwusingutils::Sweaveon Jan 14 2025.

Last update: 2022-02-07
Started: 2012-03-23

Readme and manuals

Help Manual

Help pageTopics
The TRAMPR Package (TRFLP Analysis and Matching Package for R)TRAMPR-package TRAMPR
Add Knowns To TRAMPknowns Databasesadd.known add.known.TRAMP add.known.TRAMPknowns combine.TRAMP combine.TRAMPknowns
Automatically Build Knowns Databasebuild.knowns
Combine Two Objectscombine
Combine TRAMPsamples Objectscombine.TRAMPsamples
Calculate Matrix of Distances between Peakscreate.diffsmatrix
Demonstration Knowns Databasedemo.knowns
Demonstration Samples Databasedemo.samples
Knowns Clusteringgroup.knowns group.knowns.TRAMP group.knowns.TRAMPknowns
Load ABI Output Filesload.abi load.abi.create.info load.abi.create.template peakscanner.to.genemapper
Plot a TRAMP Objectplot.TRAMP TRAMP.plotone
Summary Plot of Knowns Dataplot.TRAMPknowns
Plot a TRAMPsamples Objectplot.TRAMPsamples TRAMPsamples.plotone
Read ABI Output Filesread.abi
Read/Write TRAMPknowns and TRAMPsamples Objectsread.TRAMPknowns read.TRAMPsamples write.TRAMPknowns write.TRAMPsamples
Rebuild a TRAMP Objectrebuild.TRAMP
Mark a TRAMP Match as Ignoredremove.TRAMP.match
Create Presence/Absence Matrices from TRAMP Objectssummary.TRAMP
TRFLP Analysis and Matching ProgramTRAMP
Index (Subset) TRAMPsamples and TRAMPknowns ObjectsTRAMPindexing [.TRAMPknowns [.TRAMPsamples
TRAMPknowns Objectslabels.TRAMPknowns summary.TRAMPknowns TRAMPknowns
TRAMPsamples Objectslabels.TRAMPsamples summary.TRAMPsamples TRAMPsamples
Interactively Alter a TRAMP Objectupdate.TRAMP