README.md

frulhns

DOI

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

Cell, 155(7):1610-1623, 19 December 2013 doi: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:

Installation

Choose the Released versions instructions unless you want to keep up with package development.

Released versions

There is presently no version on CRAN, but the package can be installed from our lab R repository.

# first install frulhns R package and its dependencies
# dependencies = TRUE will install suggested packages that are
# required for building vignettes.
install.packages('frulhns',repos=c(getOption("repos"),'http://jefferislab.org/R'),
                 type='both',dependencies=TRUE)
# now you can use the package to explore our data
library(frulhns)

Bleeding Edge

You can also use the devtools package to install the development versions of this package and its main dependencies:

if (!require("devtools")) install.packages("devtools")

# install non-CRAN dependencies explicitly
devtools::install_github("jefferis/gphys")
# dependencies = TRUE will install suggested packages from CRAN that are required for the vignettes.
devtools::install_github("jefferis/frulhns", dependencies=TRUE)

Note: Windows users need Rtools in addition to devtools to install this way.

Install details

Dependencies

See 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, my gphys package and nat packages and the CRAN 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 as an installation option with the exception of packages not available on CRAN.

AnalysisSuite

The neuroanatomical analysis in the neurons vignette depend only on my 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 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.

If you wish to use the AnalysisSuite code to replicate analysis from Kohl, Ostrovsky et al 2013 exactly as it was performed, you must install and load the 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 package homepage.



jefferis/frulhns documentation built on May 17, 2017, 4:04 p.m.