Installed Software

Information about the extra software packages we have installed.

samtools, SAM/BAM file library and utilites
bowtie, sequence read mapper
cufflinks, RNA-Seq differential expression analysis
tophat, splice junction mapper
bioconductor, meta-package for R bioinformatics
BLAST+, sequence alignment tool. (well actually we have older version)
GraphViz, graph visiualization toolkit
librdf, RDF toolkit
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