ArticleBioinformatics (Oxford, England)2023
ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed.
- Article
- ChemGenXplore: an interactive tool for exploring and analysing chemical genomic data.Bioinformatics (Oxford, England) · 2026Article
- Simple large-scale quantitative phenotyping and antimicrobial susceptibility testing with Q-PHAST.Nature protocols · 2026Review
- High-throughput chemical genomic screening: a step-by-step workflow from plate to phenotype.mSystems · 2025Article
- Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationHigh-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 ChemGAPP to bridge this gap. ChemGAPP integrates various steps in a streamlined and user-friendly format, including rigorous quality control measures to curate screening data.
resultsChemGAPP provides three sub-packages for different chemical-genomic screens: ChemGAPP Big for large-scale screens; ChemGAPP Small for small-scale screens; and ChemGAPP GI for genetic interaction screens. ChemGAPP Big, tested against the Escherichiacoli KEIO collection, revealed reliable fitness scores which displayed biologically relevant phenotypes. ChemGAPP Small demonstrated significant changes in phenotype in a small-scale screen. ChemGAPP GI was benchmarked against three sets of genes with known epistasis types and successfully reproduced each interaction type. AVAILABILITY AND IMPLEMENTATION: ChemGAPP is available at https://github.com/HannahMDoherty/ChemGAPP, as a standalone Python package as well as Streamlit applications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.