Chemical genetic data analysis pipeline for the Escherichia coli genetic reference panel (EcoRef). The phenotypic data comes in the form of solid agar plate colonies. The pipeline takes care of spotting possible contaminations in the plates and errors in the colony recognition, as well as picking the optimal time piint for each condition. The actual phenotypic score is carried out by the EMAP matlab library, which the user should run after the first steps of the pipeline. Subsequent steps take care of normalizing the data as well as deriving FDR-corrected p-values for each growth phenotype.

The pipeline and scripts come with limited documentation and is intended to work for the EcoRef screening only, even though some scripts might be useful for similar analysis. Please do get in touch with the author (Marco Galardini, [email protected]) if you need any guidance.

Colony sizes/colony opacities files, as computed by Iris are needed as inputs (provided in the batch5.tar.gz and batch6.tar.gz files).

The makefile contains the various bits of the pipeline:

• make select will scan the Iris files and pick the optimal timepoint for each condition and replica
• make collect will collect the Iris files corresponding to the selected timepoints
• make pre-process will remove artifacts generated by Iris and possible plate contaminations
• (here the user is expected to run EMAP on the results of the make pre-process step)
• make post-process will normalize the S-scores as computed by EMAP, as well as compute FDR-corrected p-value for each S-score
• make deletion will process the S-scores derived from a chemical genomics screening

• python (2.7+ AND 3.3+), plus the following libraries:
  • pandas
  • numpy
  • scipy
  • fastcluster
  • statsmodels
  • networkx

Copyright (C) <2015> EMBL-European Bioinformatics Institute

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Neither the institution name nor the name screenings can be used to endorse or promote products derived from this software without prior written permission. For written permission, please contact [email protected].

Products derived from this software may not be called screenings nor may screenings appear in their names without prior written permission of the developers. You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.