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    * [[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

WoldlabWiki: Documentation/InstalledSoftware (last edited 2012-09-17 17:49:32 by hamrhein)