User:Konrad U Foerstner/Tools and procedures
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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
- Tips:
- small count noise - sequence deeper
- large count noise - sequence more replicates
- if the assumption that most genes are not differentially expressed is not the case use different methods to normalize (e.g. spike-ins)
Others
- BaySEq
- edgR
- Gfold
- NoiSeq
Python
General useful libraries
- BioPython
- bx-python
- NumPy/SciPy
- numexpr Fast numerical array expression evaluator for Python and NumPy
- panda
- beautiful soup
- matplotlib
- ipython
- PyCogent
- fuzzywuzzy
- pattern
- pysam
- ete2 - For phylogenetic trees
- NetworkX
- h5py - HDF5 for Python
- PyTables
- Statsmodels - statistical models for Python
- scikit-learn - machine learning in Python
- PySB Python framework for Systems Biology modeling
- Augustus - system for building and scoring statistical models
- Bokeh - implementation of the "Grammar of Graphics"
- PyMC - Bayesian inference in Python
- matplotlib-venn - Venn diagrams in matplotlib
