SwimR: SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
Version 1.14.0

SwimR is an R-based suite that calculates, analyses, and plots the frequency of C. elegans swimming behavior over time. It places a particular emphasis on identifying paralysis and quantifying the kinetic elements of paralysis during swimming. Data is input to SwipR from a custom built program that fits a 5 point morphometric spine to videos of single worms swimming in a buffer called Worm Tracker.

AuthorJing Wang <jing.wang.2@vanderbilt.edu>, Andrew Hardaway <hardawayja@gmail.com> and Bing Zhang <bing.zhang@vanderbilt.edu>
Bioconductor views Visualization
Date of publicationNone
MaintainerRandy Blakely <Randy.Blakely@vanderbilt.edu>
LicenseLGPL-2
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SwimR")

Getting started

Package overview

Popular man pages

createFrequencyMatrix: Analyzing the frequency of worm thrashing over time and...
SwimR: Analyzing and visualizing worm swimming data
SwimR-package: SwimR: A Suite of Analytical Tools for Quantification of C....
See all...

All man pages Function index File listing

Man pages

createFrequencyMatrix: Analyzing the frequency of worm thrashing over time and...
SwimR: Analyzing and visualizing worm swimming data
SwimR-package: SwimR: A Suite of Analytical Tools for Quantification of C....

Functions

SwimR Man page Source code
SwimR-package Man page
createFrequencyMatrix Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/SwimR.R
R/createFrequencyMatrix.R
build
build/vignette.rds
inst
inst/doc
inst/doc/SwimR.R
inst/doc/SwimR.Rnw
inst/doc/SwimR.pdf
inst/extdata
inst/extdata/SwimExample
inst/extdata/SwimExample/SwimR_Matrix.txt
inst/extdata/SwimExample/SwimR_anno.txt
inst/extdata/trackerFiles
inst/extdata/trackerFiles/N2_M9_10-14-11_1-1.txt
inst/extdata/trackerFiles/N2_M9_10-14-11_2-1.txt
inst/extdata/trackerFiles/N2_M9_10-14-11_3-1.txt
inst/extdata/trackerFiles/N2_M9_10-14-11_4-1.txt
inst/extdata/trackerFiles/N2_M9_10-14-11_5-1.txt
inst/extdata/trackerFiles/dat-1_(ok157)_1-10-11_1-1.txt
inst/extdata/trackerFiles/dat-1_(ok157)_1-10-11_2-1.txt
inst/extdata/trackerFiles/dat-1_(ok157)_1-11-11_1-1.txt
inst/extdata/trackerFiles/dat-1_(ok157)_1-11-11_4-1.txt
inst/extdata/trackerFiles/dat-1_(ok157)_1-12-11_3-1.txt
man
man/SwimR-package.Rd
man/SwimR.Rd
man/createFrequencyMatrix.Rd
vignettes
vignettes/Figure1.jpg
vignettes/Figure2.jpg
vignettes/Figure3.jpg
vignettes/Figure4.jpg
vignettes/Figure5.jpg
vignettes/Figure6.jpg
vignettes/SwimR.Rnw
SwimR documentation built on May 20, 2017, 10:05 p.m.

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