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TOPS
A user friendly tool for Interaction Data Analysis
TOPS is short for Tool for Combination Perturbation Screen Analysis and strives to be a benchtop-scientist-friendly data analysis, filtering and visualization tool primarily for functional genomics screening data.
We support data derived from Luminex multiplexing as described in our Nature Chemical Biology paper or from shRNA screens using Massively Parallel Sequencing natively. However the input file format for TOPS is simple and basically any data that follow the general format:
Name of interaction partner A, Name of interaction partner B, numerical score
.. can be imported and analyzed, plotted, filtered and explored with TOPS.
TOPS 1.01: minor spelling mistakes in the help files have been corrected
TOPS 1.1.2: a bug in the linear model scripts that lead to a crash if less than 2 replicates are left after filtering has been fixed.
TOPS 1.1.3: Change to the linear model scripts. The scripts now exclude all samples with less than 2 replicates remaining after filtering and log the filtered items.
TOPS 1.1.3.1: Minor tweak in the two analysis scripts linearRegression.R and linearRegression_split.R
Last edit: Markus Muellner 2014-01-28
In case of problems starting TOPS (doubleclick on the executeable does not result in program start) please check if you have the correct java setup.
TOPS runs with the 32 bit version of Java but may, depending on version, experience issues with the 64 bit one.