To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("SwimR")
In most cases, you don't need to download the package archive at all.
SwimR
SwimR: A Suite of Analytical Tools for Quantification of C. elegans Swimming Behavior
Bioconductor version: 2.14
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 (from within R,
enter citation("SwimR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("SwimR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SwimR")
| R Script | SwimR | |
| Reference Manual |
Details
| biocViews | Software, Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| 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 |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SwimR_1.2.0.tar.gz |
| Windows Binary | SwimR_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | SwimR_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | SwimR_1.2.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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