Wold Lab|
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| Deletions are marked like this. | Additions are marked like this. |
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| * [[http://www.graphviz.org/ | GraphViz ]], graph visualization toolkit | * [[http://www.graphviz.org/ | GraphViz ]], (>2.20.2) graph visualization toolkit |
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| * redland / librdf > 1.0.14 * redland language binding, python > 1.0.14 * libraptor > 2.0.6 * librasqal > 0.9.28 |
* redland / librdf (> 1.0.14) * redland language binding, python (> 1.0.14) * libraptor (> 2.0.6) * librasqal (> 0.9.28) |
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| * [[http://ipython.org/ | ipython ]], > 0.12, enhanced python shell | * [[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, (>2.20.2) 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