TRAMPR: 'TRFLP' Analysis and Matching Package for R

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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.

Author
Rich FitzJohn & Ian Dickie
Date of publication
2016-06-09 13:17:58
Maintainer
Rich FitzJohn <rich.fitzjohn@gmail.com>
License
GPL-2
Version
1.0-8

View on CRAN

Man pages

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

Files in this package

TRAMPR
TRAMPR/inst
TRAMPR/inst/CITATION
TRAMPR/inst/demo_samples_abi_soilcore.csv
TRAMPR/inst/demo_samples_abi_template_full.csv
TRAMPR/inst/demo_samples_abi.txt
TRAMPR/inst/demo_samples_abi_info_full.csv
TRAMPR/inst/doc
TRAMPR/inst/doc/TRAMPRdemo.pdf
TRAMPR/inst/doc/TRAMPRdemo.Rnw
TRAMPR/inst/doc/TRAMPRdemo.R
TRAMPR/NAMESPACE
TRAMPR/data
TRAMPR/data/demo.samples.rda
TRAMPR/data/demo.knowns.rda
TRAMPR/R
TRAMPR/R/load.abi.R
TRAMPR/R/TRAMP.R
TRAMPR/R/TRAMPknowns.R
TRAMPR/R/TRAMPsamples.R
TRAMPR/R/read.write.R
TRAMPR/R/util.R
TRAMPR/vignettes
TRAMPR/vignettes/TRAMPRdemo.Rnw
TRAMPR/MD5
TRAMPR/build
TRAMPR/build/vignette.rds
TRAMPR/DESCRIPTION
TRAMPR/ChangeLog
TRAMPR/man
TRAMPR/man/read.abi.Rd
TRAMPR/man/update.TRAMP.Rd
TRAMPR/man/remove.TRAMP.match.Rd
TRAMPR/man/combine.Rd
TRAMPR/man/demo.samples.Rd
TRAMPR/man/classify.Rd
TRAMPR/man/build.knowns.Rd
TRAMPR/man/demo.knowns.Rd
TRAMPR/man/TRAMPR-package.Rd
TRAMPR/man/read.write.Rd
TRAMPR/man/plot.TRAMP.Rd
TRAMPR/man/TRAMPsamples.Rd
TRAMPR/man/TRAMPindexing.Rd
TRAMPR/man/absolute.min.Rd
TRAMPR/man/TRAMPknowns.Rd
TRAMPR/man/plot.TRAMPknowns.Rd
TRAMPR/man/add.known.Rd
TRAMPR/man/plot.TRAMPsamples.Rd
TRAMPR/man/TRAMP.Rd
TRAMPR/man/rebuild.TRAMP.Rd
TRAMPR/man/group.knowns.Rd
TRAMPR/man/summary.TRAMP.Rd
TRAMPR/man/combine.TRAMPsamples.Rd
TRAMPR/man/create.diffsmatrix.Rd
TRAMPR/man/load.abi.Rd