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ChemGAPP; A Package for Chemical Genomics Analysis and Phenotypic Profiling.

Doherty, H. M.; Kritikos, G.; Galardini, M.; Banzhaf, M.; Moradigaravand, D.

2023-01-06 bioinformatics
10.1101/2023.01.05.522861 bioRxiv
Show abstract

High-throughput chemical genomic screens produce informative datasets, providing valuable insights into unknown gene function on a genome-wide level. However, there is currently no comprehensive analytic package publicly available. We developed and benchmarked ChemGAPP to bridge this gap. ChemGAPP allows integration of various steps in a streamlined and user-friendly format, including rigorous quality control measures to curate screening data. ChemGAPP provides three sub-packages for different chemical-genomic screens: ChemGAPP Big for handling large-scale high-throughput screens; ChemGAPP Small, designed for small-scale screen analysis and ChemGAPP GI for genetic interaction screen analysis. ChemGAPP is available at https://github.com/HannahMDoherty/ChemGAPP.

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The top 8 journals account for 50% of the predicted probability mass.

1
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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.