Wold Lab|
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| * redland language binding, python > 1.0.14 | |
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| * [[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 |
* [[http://matplotlib.sourceforge.net | matplotlib ]], (> 0.99.1.2) python plotting library * [[http://numpy.scipy.org | NumPy ]], (> 1.3.0) python scientific computing package * [[http://networkx.lanl.gov/ | Network X]], (> 0.99) python graph library * [[http://networkx.lanl.gov/pygraphviz/ | PyGraphViz]], (> 0.99) python bridge to graphviz * [[http://ipython.org/ | ipython ]], > 0.12, enhanced python shell |
Installed Software
Information about the extra software packages we have installed.
samtools, (1.18), SAM/BAM file library and utilites
bowtie, (0.9.9.2), sequence read mapper
cufflinks (1.3.0), RNA-Seq differential expression analysis
tophat, (1.3.3) splice junction mapper
R CRAN home page, (latest) installable R packages
bioconductor, (latest) meta-package for R bioinformatics
BLAST+, sequence alignment tool. (well actually we have older version)
GraphViz, graph visualization toolkit
librdf, RDF toolkit
redland / librdf > 1.0.14
redland language binding, python > 1.0.14
libraptor > 2.0.6
librasqal > 0.9.28
UCSC Genome Browser, various utilities and libraries from UCSC
eXpress, Streaming quantification for high-throughput sequencing
- Python packages
matplotlib, (> 0.99.1.2) python plotting library
NumPy, (> 1.3.0) python scientific computing package
Network X, (> 0.99) python graph library
PyGraphViz, (> 0.99) python bridge to graphviz
ipython, > 0.12, enhanced python shell