https://github.com/jefferis/analysissuite

R Neuron Analysis Suite provides functions to read/write/analyse neuroanatomical data
https://github.com/jefferis/analysissuite

Last synced: 27 days ago
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R Neuron Analysis Suite provides functions to read/write/analyse neuroanatomical data

• Host: GitHub
• URL: https://github.com/jefferis/analysissuite
• Owner: jefferis
• License: other
• Created: 2010-09-04T21:37:32.000Z (about 14 years ago)
• Default Branch: master
• Last Pushed: 2019-08-20T11:05:36.000Z (about 5 years ago)
• Last Synced: 2023-10-20T20:43:05.544Z (about 1 year ago)
• Language: R
• Homepage: http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:start
• Size: 32.6 MB
• Stars: 6
• Watchers: 2
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
**NB most AnalysisSuite functionality has been superseded by the much more modern [nat R package](http://natverse.github.io/nat/) however this code is still of more than historical interest since a small amount of functionality has not been ported to nat.**

This package provides numerous functions for reading/writing and analysing neuroanatomical data in R.  It is an update to accompany the paper:

Cachero, Ostrovsky et al., Sexual Dimorphism in the Fly Brain, Current Biology (2010), doi:10.1016/j.cub.2010.07.045

http://dx.doi.org/10.1016/j.cub.2010.07.045

of software first released for the paper:

"Comprehensive Maps of Drosophila Higher Olfactory Centers: 

Spatially Segregated Fruit and Pheromone Representation"

Cell (2007), doi:10.1016/j.cell.2007.01.040

by Gregory S.X.E. Jefferis*, Christopher J. Potter*

Alexander M. Chan, Elizabeth C. Marin

Torsten Rohlfing, Calvin R. Maurer, Jr., and Liqun Luo

http://dx.doi.org/10.1016/j.cell.2007.01.040

R Install

=========

Make sure you have a recent version of R installed (R>=2.15.1 recommended). Choose from one of the 3 install

methods below and then see **Running AnalysisSuite in R**.

Easy Install

------------

This is the recommended installation method if you just want to try this out. 

This code changes frequently, so for regular use, the Developer install is recommended. 

  * Start R

  * `source("http://flybrain.mrc-lmb.cam.ac.uk/R/AnalysisSuite/WebInstall.R")`

    * You will be asked to choose an install/download location for the source code

    * R unfortunately doesn't have a function to choose a directory, so once you have

      selected your directory you will have to type a fake filename and then click "Save"

  * R will download my code and install a lot of required packages

  * Now go to **Running AnalysisSuite in R**

Manual Install

--------------

You should only need do this if the Easy Install fails

  * Download this repository as [zip file](https://github.com/jefferis/AnalysisSuite/zipball/master)

  * Unzip the zip file in /path/to/some/sensible/directory

  * Start R

  * Source `/path/to/some/sensible/directory/AnalysisSuite/R/Install.R`

    * Either use the File ... Source File menu and choose the file in the GUI

    * or `source('/path/to/some/sensible/directory/AnalysisSuite/R/Install.R')` at the command line

  * Now go to **Running AnalysisSuite in R**

  

Developer Install

-----------------

This is strongly recommended if you plan to use this code on a regular basis

  * Make sure you have a recent version of R installed (R>=2.15.1 recommended)

  * Install [git](http://git-scm.com/) if you don't already have it

  * In a shell/terminal session

    * `cd /path/to/some/sensible/directory`

    * `git clone https://github.com/jefferis/AnalysisSuite.git`

  * Start R

  * `source('/path/to/some/sensible/directory/AnalysisSuite/R/Install.R')`

  * Now go to **Running AnalysisSuite in R**

Running AnalysisSuite in R

==========================

  * You can now start AnalysisSuite (in this and future R sessions) by doing 

     `source(getOption('gjanalysissuite.startup'))`

  * See [our wiki](http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:start) for further details.

Moving the location of AnalysisSuite

-----------------------------------

If you move the AnalysisSuite directory on your filesystem just source `AnalysisSuite/R/Install.R` again to update

the path to AnalysisSuite.

Amira Installation

==================

There are a few useful Amira scripts located in the amira subdirectory.

  * See instructions in the readme in amira subdirectory

  * Essentially run Install.hx script