2018koyeast

Analysis on chemical genomics data across 4 yeast strains.

Note

The s-scores for the 1000 yeast collection is missing from the paper's supplementary materials: find it here (out/yeast_scores.txt.gz). Raw and normalized colony sizes can also be found in theis repository (here out/yeasts_natural_colony_sizes.tsv.gz).

Also, for convenience, the corrected colony sizes are available through FigShare.

Introduction

This repository contains the reproducible pipeline that starts from the chemical genomics data to the final summary plots. Part of the data is generated prior to this repository (e.g. the s-scores and the gene disruption score for the yeast natural isolates). The pipeline is based on a snakemake, with the exception of the jupyter notebooks, which have to be run one by one. Most of the steps involve a script present in the src directory, which are mostly based on python 3 and the following libraries:

• numpy
• scipy
• pandas
• scikit-learn
• statsmodels
• biopython
• limix
• xarray
• DendroPy

If jupyter notebooks are used, the matplotlib and seaborn python libraries are also required.

Usage

Provided that all input files are present the whole pipeline can be run by typing: snakemake -p all. You can add --cores XX to parallelize some steps. Please make sure you have at least 12Gb of RAM available.

Citation

Galardini, Marco, Bede P. Busby, Cristina Vieitez, Alistair S. Dunham, Athanasios Typas, and Pedro Beltrao. "The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae." Molecular Systems Biology 15, no. 12 (2019).

Copyright

Copyright 2018 EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.