User:Konrad U Foerstner/Tools and procedures: Difference between revisions
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== NGS == | == NGS == | ||
* [https://github.com/lomereiter/sambamba] - offers similar functions as samtools but offers parallel processing | * [https://github.com/lomereiter/sambamba sambamba] - offers similar functions as samtools but offers parallel processing | ||
=== SNP calling === | === SNP calling === | ||
| Line 8: | Line 8: | ||
* Important. Base alignment quality (BAQ) is switched on per default and very (too) strict [http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html 5 Things to Know About SAMtools Mpileup] | * Important. Base alignment quality (BAQ) is switched on per default and very (too) strict [http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html 5 Things to Know About SAMtools Mpileup] | ||
== Phylogenetic trees == | == Phylogenetic trees == | ||
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* [http://pandas.pydata.org/ panda] | * [http://pandas.pydata.org/ panda] | ||
* [http://www.crummy.com/software/BeautifulSoup/ beautiful soup] | * [http://www.crummy.com/software/BeautifulSoup/ beautiful soup] | ||
* [http://pypi.python.org/pypi/bioservices BioServices] | |||
* [http://matplotlib.org/ matplotlib] | * [http://matplotlib.org/ matplotlib] | ||
* [http://ipython.org/ ipython] | * [http://ipython.org/ ipython] | ||
| Line 89: | Line 89: | ||
* [https://github.com/daler/gffutils gffutils] | * [https://github.com/daler/gffutils gffutils] | ||
* [https://github.com/alimanfoo/pysamstats pysamstats] | * [https://github.com/alimanfoo/pysamstats pysamstats] | ||
* [https://vincent.readthedocs.org/ Vincent] - A Python to Vega Translator | |||
* [https://github.com/mwaskom/seaborn Seaborn] - statistical data visualization | |||
=== Misc === | === Misc === | ||
Latest revision as of 12:07, 20 November 2013
NGS
- sambamba - offers similar functions as samtools but offers parallel processing
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
- BioServices
- 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
- gffutils
- pysamstats
- Vincent - A Python to Vega Translator
- Seaborn - statistical data visualization
Misc
Visualisation
- Circos
- ColorBrewer
- D3.js
- corrplot - R package to visualize correlations
