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

• Text editor
  • JEdit: http://www.jedit.org/index.php
  • VIM: http://www.vim.org
  • notepad++: http://notepad-plus-plus.org/ (Windows only)
  • TextMate: http://macromates.com/ (Mac only)

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. (FYI, you can use them on Mac & Linux).

• 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/
• Matplotlib - http://www.matplotlib.org (python library for plotting)
  • Check out its gallary at http://matplotlib.org/gallery.html

Programs used in the server side mostly

• Text editor in 'Terminal Mode'
  • emacs (Cheat Sheet)
  • Vim (Cheat Sheet)
  • 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).
• ProteoWizard (format converting tool)

Basic sequence analysis

• NCBI BLAST (See also BLAST+_HowTo)
• BLAT
• GMAP
• MUSCLE
• USEARCH