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← Revision 14 as of 2012-09-17 17:49:32 ⇥
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* [[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://samtools.sourceforge.net/ | samtools ]], (0.1.18), SAM/BAM file library and utilites * [[http://bowtie-bio.sourceforge.net/index.shtml | bowtie ]], (0.12.7), sequence read mapper |
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* [[http://tophat.cbcb.umd.edu/ | tophat ]], (1.3.3) splice junction mapper | * [[http://tophat.cbcb.umd.edu/ | tophat ]], (1.4.0) splice junction mapper |
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* [[http://www.graphviz.org/ | GraphViz ]], graph visiualization toolkit | * [[http://www.graphviz.org/ | GraphViz ]], (>2.20.2) graph visualization 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 |
* redland / librdf (> 1.0.14) * redland language binding, python (> 1.0.14) * libraptor (> 2.0.6) * librasqal (> 0.9.28) * [[http://genome.ucsc.edu | UCSC Genome Browser ]], (v272) various utilities and libraries from UCSC * [[http://bio.math.berkeley.edu/eXpress | eXpress ]], (1.1.1) Streaming quantification for high-throughput sequencing |
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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 * [[http://code.google.com/p/pysam/ | Pysam ]], (>= 0.6), python interface to sam/bam files |
Installed Software
Information about the extra software packages we have installed.
samtools, (0.1.18), SAM/BAM file library and utilites
bowtie, (0.12.7), sequence read mapper
cufflinks (1.3.0), RNA-Seq differential expression analysis
tophat, (1.4.0) 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, (v272) various utilities and libraries from UCSC
eXpress, (1.1.1) 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
Pysam, (>= 0.6), python interface to sam/bam files