Difference between revisions of "List of programs"
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== Short-read sequencing data analysis == | == Short-read sequencing data analysis == | ||
* bowtie | * bowtie | ||
| + | * bowtie2 | ||
* tophat | * tophat | ||
* cufflink | * cufflink | ||
| + | * STAR | ||
* MACS | * MACS | ||
* HOMER | * HOMER | ||
Revision as of 14:10, 23 April 2014
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
- bowtie2
- tophat
- cufflink
- STAR
- MACS
- HOMER
Shotgun Proteomics data analysis
- MS-GF+
- COMET
- X!Tandem
- MaxQuant & Persus (it only supports Windows because of .NET framework dependency).
- msconvert
