SwimR
This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see SwimR.
SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
Bioconductor version: 3.12
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>
citation("SwimR")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("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")| SwimR | R Script | |
| Reference Manual |
Details
| biocViews | Software, Visualization |
| Version | 1.28.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SwimR_1.28.0.tar.gz |
| Windows Binary | SwimR_1.28.0.zip |
| macOS 10.13 (High Sierra) | SwimR_1.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SwimR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SwimR |
| Bioc Package Browser | https://code.bioconductor.org/browse/SwimR/ |
| Package Short Url | https://bioconductor.org/packages/SwimR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.12 | Source Archive |