• Documentation
• InstalledSoftware

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