jefferis / bigneuronimperial

Some analysis associated with the BigNeuron hackathon at Imperial College Jan 2016

bigneuronimperial

Some analysis associated with the BigNeuron hackathon at Imperial College Jan 2016

This code is provided as R Markdown documents.

Install

You should install:

1. R from http://www.r-project.org/ (Latest R >3.2.1 recommended)
2. RStudio from http://www.rstudio.com.

Open the binimperial2016.Rproj file in Rstudio

You will then need to install some R packages from inside R. One package containing the Neuroanatomy ToolBox nat must be installed from github like so:

# install devtools if required
if (!require("devtools")) install.packages("devtools")
# then install nat
devtools::install_github("jefferis/nat")

Other packages can be installed via the gui or command line:

# also install some regular packages
install.packages(c("dplyr","knitr"))

Use

1. Make sure that the gold_trainingsubset_79_all folder containing the swc files distributed on Wed is in the same folder as the Rmd files.
2. Press the "Knit" button for the 01-findswcs.Rmd file
3. Repeat with 02-bigneuronqc.Rmd