Software

Decombinator: a tool for analysing T cell receptor sequences

Decombinator: a tool for fast, efficient gene assignment in T cell receptor sequences using a finite state machine (Bioinformatics, 2013)

Niclas Thomas, James Heather, Wilfred Ndifon, John Shawe-Taylor & Benny Chain.

Source code for Decombinator is available here.

A stand-alone executable for Windows can be downloaded below. Instructions can be found here. If your platform is not supported or you have trouble running the executable on your system, we recommend downloading the source code from GitHub using the link above, and implementing Decombinator through Python.

Decombinator v1.4 for Windows

agilp: Agilent expression array processing package


agilp: Agilent expression array processing package, (2012), R package version 3.0.0, Bioconductor.

Benny Chain

 

MDI score: a tool to assess the sensitivity and specificity of your transcriptional modules

A simple set of R scripts that will assess the confidence a user can have in a transcriptional module to reliably deconvolute biological information from a multicellular transcriptomic dataset.

Gabriele Pollara, Matthew J. Murray, James M. Heather, Rachel Byng-Maddick, Naomi Guppy, Matthew Ellis, Carolin T. Turner, Benjamin M. Chain, Mahdad Noursadeghi

Reference: Validation of Immune Cell Modules in Multicellular Transcriptomic Data

Code on Github for download