Software

Decombinator

Decombinator is a string-matching finite state machine designed for the rapid search, analysis and assignment of the T Cell Receptor repertoire in high-throughput sequence data. Decombinator is free, open source, and available for use on Github.

Published in: Thomas et al, (Bioinformatics, 2013)
Authors: James M. Heather, Niclas Thomas, Katharine Best, Theres Oakes, Mazlina Ismail, Thomas Peacock and Benny Chain
 

Agilp

Agilp is an Agilent expression array processing package, written in R for the Bioconductor project. Agilp documentation is available here. Agilp is free, open source, and available for use on Github.

Authors: Benny Chain
 

MDI Score

MDI Score is a tool to assess the sensitivity and specificity of transcriptional modules. MDI Score consists of a simple set of R scripts that assess the reliability of a transcriptional module to accurately deconvolute biological information from a multicellular transcriptomic dataset.

Published in: Pollara et al, (PLOS ONE, 2017). MDI Score is free, open source, and available for use on Github.
Authors: Gabriele Pollara, Matthew J. Murray, James M. Heather, Rachel Byng-Maddick, Naomi Guppy, Matthew Ellis, Carolin T. Turner, Benny Chain, Mahdad Noursadeghi