User:Konrad U Foerstner/Tools and procedures: Difference between revisions
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* [https://github.com/seatgeek/fuzzywuzzy fuzzywuzzy] | * [https://github.com/seatgeek/fuzzywuzzy fuzzywuzzy] | ||
* [https://github.com/clips/pattern pattern] | * [https://github.com/clips/pattern pattern] | ||
* [https://code.google.com/p/pysam/ pysam] | |||
* [http://packages.python.org/ete2/index.html ete2] - For phylogenetic trees | * [http://packages.python.org/ete2/index.html ete2] - For phylogenetic trees | ||
Revision as of 06:38, 13 December 2012
SNP calling
With Samtools
- Important. Base alignment quality (BAQ) is switched on per default and very (too) strict 5 Things to Know About SAMtools Mpileup
TSS prediction
- TSSi (untested)
Pathway visualization
- iPath2.0 (by Takuji!) - the modified and original maps can be downloaded as SVG (e.g. full metabolic map)
- KEGG Mapper (untested)
Trascription Terminator prediction
Python
General useful libraries
- BioPython
- bx-python
- NumPy/SciPy
- panda
- statsmodels
- beautiful soup
- matplotlib
- ipython
- PyCogent
- fuzzywuzzy
- pattern
- pysam
- ete2 - For phylogenetic trees
