User:Konrad U Foerstner/Tools and procedures: Difference between revisions
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[http://cegg.unige.ch/mirmap/ miRmap] (untested) | [http://cegg.unige.ch/mirmap/ miRmap] (untested) | ||
== Differential gene expression analysis == | |||
=== DESeq === | |||
* [http://bioconductor.org/packages/release/bioc/html/DESeq.html DeSeq] | |||
* small count noise - sequence deeper | |||
* large count noise - sequence more replicates | |||
=== Others === | |||
* BaySEq | |||
* edgR | |||
* Gfold | |||
* NoiSeq | |||
== Python == | == Python == | ||
Revision as of 04:22, 26 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)
Differential gene expression analysis
DESeq
- small count noise - sequence deeper
- large count noise - sequence more replicates
Others
- BaySEq
- edgR
- Gfold
- NoiSeq
Python
General useful libraries
- BioPython
- bx-python
- NumPy/SciPy
- panda
- statsmodels
- beautiful soup
- matplotlib
- ipython
- PyCogent
- fuzzywuzzy
- pattern
- pysam
- ete2 - For phylogenetic trees
