https://github.com/jefferis/bigneuronimperial

Some analysis associated with the BigNeuron hackathon at Imperial College Jan 2016
https://github.com/jefferis/bigneuronimperial

Last synced: 27 days ago
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Some analysis associated with the BigNeuron hackathon at Imperial College Jan 2016

• Host: GitHub
• URL: https://github.com/jefferis/bigneuronimperial
• Owner: jefferis
• Created: 2016-01-21T00:35:41.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2016-01-22T18:34:07.000Z (almost 9 years ago)
• Last Synced: 2023-04-16T09:10:56.115Z (over 1 year ago)
• Size: 9.77 KB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# bigneuronimperial

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

This code is provided as [R Markdown documents](http://rmarkdown.rstudio.com).

## 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](https://github.com/jefferis/nat) must be installed 

from github like so:

```r

# 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:

```r

# 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`