Difference between revisions of "List of programs"
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TaejoonKwon (Talk | contribs) (→Programs used in the server side mostly) |
TaejoonKwon (Talk | contribs) (→Basic tools) |
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** Mac: [http://cyberduck.io/ Cyberduck] is a GUI client. | ** Mac: [http://cyberduck.io/ Cyberduck] is a GUI client. | ||
** Windows: [http://winscp.net/eng/index.php WinSCP] | ** Windows: [http://winscp.net/eng/index.php 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 == | == Programming == | ||
| Line 50: | Line 56: | ||
== Basic sequence analysis == | == Basic sequence analysis == | ||
| − | * | + | * [http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI BLAST] (See also [[BLAST+_HowTo]]) |
* BLAT | * BLAT | ||
* GMAP | * GMAP | ||
| + | * [http://www.drive5.com/muscle/ MUSCLE] | ||
| + | * [http://drive5.com/usearch/ USEARCH] | ||
Latest revision as of 12:55, 5 May 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
- 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'
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
