User:Konrad U Foerstner/Tools and procedures: Difference between revisions
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* [http://www.bioconductor.org/packages/2.10/bioc/html/TSSi.html TSSi] (untested) | * [http://www.bioconductor.org/packages/2.10/bioc/html/TSSi.html TSSi] (untested) | ||
== Whole genome alignments == | |||
* [http://gel.ahabs.wisc.edu/mauve/ mauve] | |||
== Pathway visualization == | == Pathway visualization == | ||
Revision as of 15:36, 15 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)
Whole genome alignments
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
