https://github.com/jefferis/frulhns
R package frulhns to accompany "A bidirectional circuit switch reroutes pheromone signals in male and female brains"
https://github.com/jefferis/frulhns
Last synced: 3 months ago
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R package frulhns to accompany "A bidirectional circuit switch reroutes pheromone signals in male and female brains"
- Host: GitHub
- URL: https://github.com/jefferis/frulhns
- Owner: jefferis
- Created: 2013-12-20T19:16:25.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2019-06-20T08:58:48.000Z (almost 6 years ago)
- Last Synced: 2025-01-16T03:33:52.058Z (4 months ago)
- Language: R
- Homepage: jefferislab.org/si/frulhns
- Size: 9.03 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# frulhns
[](http://jefferis.github.io/frulhns/)
[](https://zenodo.org/badge/latestdoi/15346264)
[](https://github.com/jefferis/frulhns/releases/latest)
[](https://travis-ci.org/jefferis/frulhns)
## Introduction
This project distributes all electrophysiological spike data, statistical analysis,
and traced neurons associated with the open access publication:
**[A bidirectional circuit switch reroutes pheromone signals in male and female brains](http://dx.doi.org/10.1016/j.cell.2013.11.025)**
_Cell_, 155(7):1610-1623, 19 December 2013 [doi:10.1016/j.cell.2013.11.025](http://dx.doi.org/10.1016/j.cell.2013.11.025)
Johannes Kohl\*, Aaron D. Ostrovsky\*, Shahar Frechter, Gregory S.X.E. Jefferis
Further information about this work, including additional data and experimental methodology, is available at http://jefferislab.org/si/frulhns. This includes cached copies of the vignettes included in this package:
* [neurons.pdf](http://jefferislab.org/si/frulhns/neurons.pdf)
* [statistics.pdf](http://jefferislab.org/si/frulhns/statistics.pdf)
## Installation
There is presently no version on CRAN,but you can use the
[**remotes**](https://cran.r-project.org/package=remotes) package
to install the development versions of this package and its dependencies:
```r
if (!requireNamespace("remotes")) install.packages("remotes")
# dependencies = TRUE will install suggested packages from CRAN that are required for the vignettes.
remotes::install_github("jefferis/frulhns", dependencies=TRUE)
```
Note: Windows users may need [Rtools](http://www.murdoch-sutherland.com/Rtools/)
in addition to [devtools](http://CRAN.R-project.org/package=devtools) to install
this way.
## Install details
### Dependencies
See [DESCRIPTION](https://github.com/jefferis/frulhns/blob/master/DESCRIPTION).
In order to build the vignettes, which are one of the main reasons
for creating this package, several additional packages are required including
[knitr](http://yihui.name/knitr/), my [gphys](https://github.com/jefferis/gphys)
package and [nat](https://github.com/jefferis/nat) packages and the CRAN
package [coin](http://cran.r-project.org/package=coin). Following standard practice,
these packages are listed under the Suggested field of the DESCRIPTION file.
They can be installed when `dependencies=TRUE` is supplied on installation.
### AnalysisSuite
The neuroanatomical analysis in the `neurons` vignette depend only on my
[nat](https://github.com/jefferis/nat) package. This is now a well-documented and
mature codebase with a number of interesting extension packages. Published work from 2013 and earlier depended on my
[AnalysisSuite](https://github.com/jefferis/AnalysisSuite)
codebase, which is not available directly as a formal R package.
This includes an earlier version of the
neuron search/similarity code now available as package
[nat.nblast](https://github.com/jefferislab/nat.nblast).
If you wish to use the AnalysisSuite code to replicate analysis from
Kohl, Ostrovsky et al 2013 exactly as it was performed at the time,
you must install and load the [nat.as](https://github.com/jefferis/nat.as)
wrapper R package, which is used to install and then load the AnalysisSuite codebase.
Full details of the installation procedure are provided on the
[nat.as](https://github.com/jefferis/nat.as) package homepage.