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* [[http://networkx.lanl.gov/ | Network X]] graph library * [[http://networkx.lanl.gov/pygraphviz/ | PyGraphViz]] python bridge to graphviz * [[http://www.graphviz.org/ | GraphViz ]] graph visiualization toolkit |
* [[http://www.graphviz.org/ | GraphViz ]], graph visiualization toolkit |
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* [[http://genome.ucsc.edu | UCSC Genome Browser ]], various utilities and libraries from UCSC * [[http://bio.math.berkeley.edu/eXpress | eXpress ]], Streaming quantification for high-throughput sequencing * Python packages * [[http://matplotlib.sourceforge.net | matplotlib ]], python plotting library * [[http://numpy.scipy.org | NumPy ]], python scientific computing package * [[http://networkx.lanl.gov/ | Network X]], python graph library * [[http://networkx.lanl.gov/pygraphviz/ | PyGraphViz]], python bridge to graphviz |
Installed Software
Information about the extra software packages we have installed.
samtools, SAM/BAM file library and utilites
bowtie, sequence read mapper
cufflinks, RNA-Seq differential expression analysis
tophat, splice junction mapper
bioconductor, meta-package for R bioinformatics
BLAST+, sequence alignment tool. (well actually we have older version)
GraphViz, graph visiualization toolkit
librdf, RDF toolkit
UCSC Genome Browser, various utilities and libraries from UCSC
eXpress, Streaming quantification for high-throughput sequencing
- Python packages
matplotlib, python plotting library
NumPy, python scientific computing package
Network X, python graph library
PyGraphViz, python bridge to graphviz