User:Konrad U Foerstner/Tools and procedures: Difference between revisions

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== SNP calling ==
== 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 17: Line 34:
* [http://www.genome.jp/kegg/mapper.html KEGG Mapper] (untested)
* [http://www.genome.jp/kegg/mapper.html KEGG Mapper] (untested)


== Trascription Terminator prediction ==
== Transcription Terminator prediction ==


* [http://transterm.cbcb.umd.edu/ TransTerm]
* [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

Phylogenetic trees

Multiple alignments

TSS prediction

Whole genome alignments

Pathway visualization

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

Misc


Visualisation

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