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

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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.

Author
Jing Wang <jing.wang.2@vanderbilt.edu>, Andrew Hardaway <hardawayja@gmail.com> and Bing Zhang <bing.zhang@vanderbilt.edu>
Date of publication
None
Maintainer
Randy Blakely <Randy.Blakely@vanderbilt.edu>
License
LGPL-2
Version
1.12.0

View on Bioconductor

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....

Files in this package

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