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ChemGAPP_Small: Chem Genomic Analysis Phenotypic Profiling

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ChemGAPP_Small: Chem Genomic Analysis Phenotypic Profiling

GitHub Repository
Health-Universe/ChemGAPP_Small
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Ready
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Updated On
ChemGAPP_Small has been produced to deal with small scale chemical genomic screens where replicates are within the plate. This differs from large chemical genomic screen where replicates are across multiple plates. ChemGAPP Small produces three types of plots, a heatmap, bar plots and swarm plots. For the bar plot and heatmap, ChemGAPP Small compares the mean colony size of within plate replicates to the mean colony size of the within plate wildtype replicates, producing a fitness ratio. The bar plots are then optionally grouped by strain or by condition. The heatmap displays all conditions and strains. For the swarm plots each mutant colony size is divided by the mean colony size of the wildtype, to produce the fitness ratio. A one-way ANOVA and Tukey-HSD analysis determines the significance in difference between each mutant fitness ratio distribution and the wildtype fitness ratio distribution. colony size can be substituted for any IRIS phenotype.

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Used as a tool for chemical genomics analysis and phenotypic profiling.Workflow: IRIS File Input ... Normalisation ... Fitness Ratio Calculation ... Data Visualization

Generalizing results to diverse organisms or conditions may be limited.

https://academic.oup.com/bioinformatics/article/39/4/btad171/7103304#401096083None

The three sub-packages of ChemGAPP were specifically crafted to facilitate broader involvement from the scientific community in chemical genomic techniques. This was achieved by streamlining the dedicated analysis pathways for each sub-package.Check out the other packages: ChemGAPP Big and GI