List of programs

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
  • Mac and Linux: Just use scp in your terminal.
  • Mac: Cyberduck is a GUI client.
  • Windows: WinSCP

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
• bowtie2
• tophat
• cufflink
• STAR
• MACS
• HOMER
• In R, Bioconductor
• In R, DESeq

Shotgun Proteomics data analysis

• MS-GF+
• COMET
• X!Tandem
• MaxQuant & Persus (it only supports Windows because of .NET framework dependency).
• msconvert