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

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* [http://packages.python.org/ete2/index.html ete2] - For phylogenetic trees
* [http://packages.python.org/ete2/index.html ete2] - For phylogenetic trees
* [http://networkx.github.com NetworkX]
* [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


=== Misc ===
=== Misc ===


* [http://messymind.net/2012/07/making-matplotlib-look-like-ggplot/ Making matplotlib look like ggplot]
* [http://messymind.net/2012/07/making-matplotlib-look-like-ggplot/ Making matplotlib look like ggplot]

Revision as of 10:55, 20 February 2013

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

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