User:Konrad U Foerstner/Tools and procedures: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
|||
| Line 37: | Line 37: | ||
== miRNA target prediction == | == miRNA target prediction == | ||
[http://cegg.unige.ch/mirmap/ miRmap] (untested) | |||
== Python == | == Python == | ||
Revision as of 05:59, 18 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
Phylogenetic trees
Multiple alignments
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)
Transcription Terminator prediction
miRNA target prediction
miRmap (untested)
Python
General useful libraries
- BioPython
- bx-python
- NumPy/SciPy
- panda
- statsmodels
- beautiful soup
- matplotlib
- ipython
- PyCogent
- fuzzywuzzy
- pattern
- pysam
- ete2 - For phylogenetic trees
