This project distributes all electrophysiological spike data, statistical analysis, and traced neurons associated with the open access publication:
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:
Choose the Released versions instructions unless you want to keep up with package development.
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)
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)
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.
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
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
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.
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