965
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1605
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Deletions are marked like this. | Additions are marked like this. |
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* [[http://samtools.sourceforge.net/ | samtools ]], SAM/BAM file library and utilites * [[http://bowtie-bio.sourceforge.net/index.shtml | bowtie ]], sequence read mapper * [[http://cufflinks.cbcb.umd.edu/ | cufflinks ]], RNA-Seq differential expression analysis * [[http://tophat.cbcb.umd.edu/ | tophat ]], splice junction mapper * [[http://www.bioconductor.org/ | bioconductor ]], meta-package for R bioinformatics |
* [[http://samtools.sourceforge.net/ | samtools ]], (1.18), SAM/BAM file library and utilites * [[http://bowtie-bio.sourceforge.net/index.shtml | bowtie ]], (0.9.9.2), sequence read mapper * [[http://cufflinks.cbcb.umd.edu/ | cufflinks ]] (1.3.0), RNA-Seq differential expression analysis * [[http://tophat.cbcb.umd.edu/ | tophat ]], (1.3.3) splice junction mapper * [[http://cran.stat.ucla.edu/banner.shtml | R CRAN home page]], (latest) installable R packages * [[http://www.bioconductor.org/ | bioconductor ]], (latest) meta-package for R bioinformatics |
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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 visualization toolkit |
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* redland / librdf > 1.0.14 * libraptor > 2.0.6 * librasqal > 0.9.28 * [[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, (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
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, python plotting library
NumPy, python scientific computing package
Network X, python graph library
PyGraphViz, python bridge to graphviz