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RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The new RSEM package (rsem-1.x) provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. It can also generate genomic-coordinate BAM files and UCSC wiggle files for visualization. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels RESM documentation
CEAS
Software for Cis-regulatory Element Annotation System.
Info at: CEAS
Installed in /cluster/tufts/ngsp/ngsp/bin
See the lib and bin directories in this directory.
You have to modify the PYTHONPATH environment variable:
set PYTHONPATH = /cluster/tufts/ngsp/ngsp/bin/lib/python2.6/site-packages/
Some supporting files including test data are available at
/cluster/tufts/ngsp/ngsp/CEAS