SwimR

DOI: 10.18129/B9.bioc.SwimR    

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

Bioconductor version: Release (3.11)

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 at vanderbilt.edu>, Andrew Hardaway <hardawayja at gmail.com> and Bing Zhang <bing.zhang at vanderbilt.edu>

Maintainer: Randy Blakely <Randy.Blakely at vanderbilt.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SwimR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SwimR")

 

PDF	R Script	SwimR
PDF		Reference Manual

Details

biocViews	Software, Visualization
Version	1.26.0
In Bioconductor since	BioC 2.13 (R-3.0) (7 years)
License	LGPL-2
Depends	R (>= 3.0.0), methods, gplots (>= 2.10.1), heatmap.plus (>= 1.3), signal (>= 0.7), R2HTML (>= 2.2.1)
Imports	methods
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SwimR_1.26.0.tar.gz
Windows Binary	SwimR_1.26.0.zip
macOS 10.13 (High Sierra)	SwimR_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SwimR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SwimR
Package Short Url	https://bioconductor.org/packages/SwimR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive