Useful Links

Here are some useful websites for cheatsheets and tutorials for:

1. UNIX

2. PYTHON

3. R

Please add (or suggest) your favourite website! Click here for instruction on how to edit. FIXME-> LINK TO EDITING WIKI

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UNIX

The basics

• An A-Z Index of the Bash command line for Unix. All the commands with a little extra information: http://www.ss64.com/bash/

• Unix/Linux Command Cheat Sheet http://fosswire.com/post/2007/08/unixlinux-command-cheat-sheet/

• Have your shell command explained: http://explainshell.com/

• A Bioinformatician's UNIX Toolbox: http://lh3lh3.users.sourceforge.net/biounix.shtml

Bioinformatics one-liners

• One-liners: https://github.com/stephenturner/oneliners

• UNIX tips: Learn 10 good UNIX usage habits: http://www.ibm.com/developerworks/aix/library/au-badunixhabits.html#one

• A linux command line reference for common operations: http://www.pixelbeat.org/cmdline.html

Learning unix

• Learning unix, material from Software Carpentry: http://software-carpentry.org/v4/shell/index.html

• Other useful material from Software Carpentry: http://software-carpentry.org/v4/index.html

• Useful tutorials from 'The Geek Stuff': http://www.thegeekstuff.com/best-of-the-blog/

Tricks and more

• Generate your .bashrc PS1 prompt easily with a drag and drop interface: <http://bashrcgenerator.com/ http://bashrcgenerator.com/>

• Cheat sheet for one-based vs zero-based coordinate systems: http://www.biostars.org/p/84686/

• Bash Shortcuts For Maximum Productivity: http://www.skorks.com/2009/09/bash-shortcuts-for-maximum-productivity/

• Using Make for reproducible scientific analyses: http://www.bendmorris.com/2013/09/using-make-for-reproducible-scientific.html

More advanced

• Testing exit values in Bash: http://blog.sanctum.geek.nz/testing-exit-values-bash/

• Bash process substitution: http://blog.sanctum.geek.nz/bash-process-substitution/

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PYTHON

The basics

• The official website: http://www.python.org/

• IPython and the IPython notebook: http://ipython.org/notebook.html

• Biopython: Python designed for bioinformatics: <http://biopython.org/wiki/Main_Page http://biopython.org/wiki/Main_Page>

• Pandas: pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language. http://pandas.pydata.org/

Python tutorials

• Learn python (interactive): http://www.learnpython.org/

• Codeacademy (interactive). Not only for learning python, but also for many other languages: http://www.codecademy.com/

• Learn python the hard way (commercial website): http://learnpythonthehardway.org/book/

• biopython tutorial: http://biopython.org/DIST/docs/tutorial/Tutorial.html

• Pandas and python. A blog on how to use pandas in python: http://manishamde.github.io/blog/2013/03/07/pandas-and-python-top-10/

• Python for biologist: A blog and tutorial website.<http://pythonforbiologists.com/? http://pythonforbiologists.com/?]

• A book on learning python: Think Python: http://www.greenteapress.com/thinkpython/

• A much larger overview of python tutorials online: https://wiki.python.org/moin/BeginnersGuide/Programmers

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R

• Starting data analysis/wrangling with R: Things I wish I'd been told: http://reganmian.net/blog/2014/10/14/starting-data-analysiswrangling-with-r-things-i-wish-id-been-told/