User:Konrad U Foerstner/Tools and procedures: Difference between revisions
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== | == NGS == | ||
=== With Samtools === | * [https://github.com/lomereiter/sambamba 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 [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 == | |||
* [http://cegg.unige.ch/newick_utils Newick Utilities] | |||
* [http://bioinf.nuim.ie/clann/ clann] | |||
* [http://evolution.genetics.washington.edu/phylip.html phylip] | |||
* [http://itol.embl.de/ iTOL] | |||
* [https://code.google.com/p/phyml/ PhyML] | |||
== Multiple alignments == | |||
* [http://www.drive5.com/muscle/ muscle] | |||
== TSS prediction == | == TSS prediction == | ||
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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 == | ||
Line 16: | Line 33: | ||
* [http://pathways.embl.de/ iPath2.0] (by Takuji!) - the modified and original maps can be downloaded as SVG (e.g. full [http://pathways.embl.de/default_maps/metabolic_map.svg metabolic map]) | * [http://pathways.embl.de/ iPath2.0] (by Takuji!) - the modified and original maps can be downloaded as SVG (e.g. full [http://pathways.embl.de/default_maps/metabolic_map.svg metabolic map]) | ||
* [http://www.genome.jp/kegg/mapper.html KEGG Mapper] (untested) | * [http://www.genome.jp/kegg/mapper.html KEGG Mapper] (untested) | ||
== Transcription Terminator prediction == | |||
* [http://transterm.cbcb.umd.edu/ TransTerm] | |||
== miRNA target prediction == | |||
[http://cegg.unige.ch/mirmap/ miRmap] (untested) | |||
== Differential gene expression analysis == | |||
=== DESeq === | |||
* [http://bioconductor.org/packages/release/bioc/html/DESeq.html 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 === | |||
* [http://biopython.org/ BioPython] | |||
* [https://bitbucket.org/james_taylor/bx-python/ bx-python] | |||
* [http://www.scipy.or NumPy/SciPy] | |||
* [https://code.google.com/p/numexpr/ numexpr] Fast numerical array expression evaluator for Python and NumPy | |||
* [http://pandas.pydata.org/ panda] | |||
* [http://www.crummy.com/software/BeautifulSoup/ beautiful soup] | |||
* [http://pypi.python.org/pypi/bioservices BioServices] | |||
* [http://matplotlib.org/ matplotlib] | |||
* [http://ipython.org/ ipython] | |||
* [http://pycogent.sourceforge.net/ PyCogent] | |||
* [https://github.com/seatgeek/fuzzywuzzy fuzzywuzzy] | |||
* [https://github.com/clips/pattern pattern] | |||
* [https://code.google.com/p/pysam/ pysam] | |||
* [http://packages.python.org/ete2/index.html ete2] - For phylogenetic trees | |||
* [http://networkx.github.com NetworkX] | |||
* [http://www.h5py.org/ h5py] - HDF5 for Python | |||
* [http://www.pytables.org PyTables] | |||
* [http://statsmodels.sourceforge.net/ Statsmodels] - statistical models for Python | |||
* [http://scikit-learn.org/stable/ scikit-learn] - machine learning in Python | |||
* [http://pysb.org/ PySB] Python framework for Systems Biology modeling | |||
* [https://code.google.com/p/augustus/ Augustus] - system for building and scoring statistical models | |||
* [https://github.com/ContinuumIO/Bokeh Bokeh] - implementation of the "Grammar of Graphics" | |||
* [https://github.com/pymc-devs/pymc PyMC] - Bayesian inference in Python | |||
* [https://pypi.python.org/pypi/matplotlib-venn matplotlib-venn] - Venn diagrams in matplotlib | |||
* [https://github.com/daler/gffutils gffutils] | |||
* [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 === | |||
* [http://messymind.net/2012/07/making-matplotlib-look-like-ggplot/ Making matplotlib look like ggplot] | |||
== Visualisation == | |||
* [http://circos.ca/ Circos] | |||
* [http://www.colorbrewer2.org/ ColorBrewer] | |||
* [http://d3js.org/ D3.js] | |||
* [http://rgm3.lab.nig.ac.jp/RGM/r_function?p=corrplot&f=corrplot corrplot] - R package to visualize correlations |
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