Package: TRAMPR 1.0-11

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_1.0-11.tar.gz
TRAMPR_1.0-11.zip(r-4.7)TRAMPR_1.0-11.zip(r-4.6)TRAMPR_1.0-11.zip(r-4.5)
TRAMPR_1.0-11.tgz(r-4.6-any)TRAMPR_1.0-11.tgz(r-4.5-any)
TRAMPR_1.0-11.tar.gz(r-4.7-any)TRAMPR_1.0-11.tar.gz(r-4.6-any)
TRAMPR_1.0-11.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
TRAMPR/json (API)

# Install 'TRAMPR' in R:

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

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

Datasets:

demo.knowns - Demonstration Knowns Database
demo.samples - Demonstration Samples Database

On CRAN:

5.06 score 23 scripts 2.5k downloads 4 mentions 39 exports 0 dependencies

Last updated from:45682bd175. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	127
source / vignettes	OK	143
linux-release-x86_64	OK	126
macos-release-arm64	OK	74
macos-oldrel-arm64	OK	66
windows-devel	OK	89
windows-release	OK	62
windows-oldrel	OK	69
wasm-release	OK	82

Exports:[.TRAMPknowns [.TRAMPsamples absolute.min add.known add.known.TRAMP add.known.TRAMPknowns build.knowns classify combine combine.TRAMP combine.TRAMPknowns combine.TRAMPsamples create.diffsmatrix group.knowns group.knowns.TRAMP group.knowns.TRAMPknowns labels.TRAMPknowns labels.TRAMPsamples load.abi load.abi.create.info load.abi.create.template plot.TRAMP plot.TRAMPknowns read.abi read.TRAMPknowns read.TRAMPsamples rebuild.TRAMP remove.TRAMP.match summary.TRAMP summary.TRAMPknowns summary.TRAMPsamples TRAMP TRAMP.plotone TRAMPknowns TRAMPsamples TRAMPsamples.plotone update.TRAMP write.TRAMPknowns write.TRAMPsamples

Dependencies:

Introduction to TRAMPR

Rendered fromTRAMPRdemo.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The TRAMPR Package (TRFLP Analysis and Matching Package for R)	TRAMPR-package TRAMPR
Add Knowns To TRAMPknowns Databases	add.known add.known.TRAMP add.known.TRAMPknowns combine.TRAMP combine.TRAMPknowns
Automatically Build Knowns Database	build.knowns
Combine Two Objects	combine
Combine TRAMPsamples Objects	combine.TRAMPsamples
Calculate Matrix of Distances between Peaks	create.diffsmatrix
Demonstration Knowns Database	demo.knowns
Demonstration Samples Database	demo.samples
Knowns Clustering	group.knowns group.knowns.TRAMP group.knowns.TRAMPknowns
Load ABI Output Files	load.abi load.abi.create.info load.abi.create.template peakscanner.to.genemapper
Plot a TRAMP Object	plot.TRAMP TRAMP.plotone
Summary Plot of Knowns Data	plot.TRAMPknowns
Plot a TRAMPsamples Object	plot.TRAMPsamples TRAMPsamples.plotone
Read ABI Output Files	read.abi
Read/Write TRAMPknowns and TRAMPsamples Objects	read.TRAMPknowns read.TRAMPsamples write.TRAMPknowns write.TRAMPsamples
Rebuild a TRAMP Object	rebuild.TRAMP
Mark a TRAMP Match as Ignored	remove.TRAMP.match
Create Presence/Absence Matrices from TRAMP Objects	summary.TRAMP
TRFLP Analysis and Matching Program	TRAMP
Index (Subset) TRAMPsamples and TRAMPknowns Objects	TRAMPindexing [.TRAMPknowns [.TRAMPsamples
TRAMPknowns Objects	labels.TRAMPknowns summary.TRAMPknowns TRAMPknowns
TRAMPsamples Objects	labels.TRAMPsamples summary.TRAMPsamples TRAMPsamples
Interactively Alter a TRAMP Object	update.TRAMP