List of programs
From XenopusBioinfo
Revision as of 14:08, 23 April 2014 by IanQuigley (Talk | contribs)
Contents
Programs you may need to install on your machine
Basic tools
- Terminal
- Mac and Linux: You already have it. Search 'Terminal'.
- Windows: PuTTY may be the best option (Download. If you love Chrome, there is an SSH app available in Chrome Web Store. (SSH shortcut is another useful extension.)
- File transfer
Programming
- Python - https://www.python.org/ version 2.7, please!
- Mac and Linux: You may have it already. Open your terminal, and type 'python -v'.
- Windows: Use Anaconda. Alternatively, you can use Enthought Canopy. These programs will make your life easier for installing important python libraries, such as numpy/scipy and matplotlib.
- Java - http://java.com/en/ (it requires to run several GUI programs & Weka)
Data visualization analysis
- Weka - http://www.cs.waikato.ac.nz/ml/weka/ (data mining & machine learning)
- IGV - http://www.broadinstitute.org/igv/home
- Cytoscape - http://www.cytoscape.org/
- R - http://www.r-project.org/
Programs used in the server side mostly
- Text editor in 'Terminal Mode'
- emacs
- vim
- nano
Short-read sequencing data analysis
- bowtie
- tophat
- cufflink
- MACS
- HOMER
Shotgun Proteomics data analysis
- MS-GF+
- COMET
- X!Tandem
- MaxQuant & Persus (it only supports Windows because of .NET framework dependency).
- msconvert