https://github.com/jefferis/AnalysisSuite
Tip revision: 87ef0795ea5417fb03aa93f9305c51a0d1856393 authored by Gregory Jefferis on 20 August 2019, 11:05:36 UTC
Update README.md
Update README.md
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README.md
**NB most AnalysisSuite functionality has been superseded by the much more modern [nat R package](http://natverse.github.io/nat/) however this code is still of more than historical interest since a small amount of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