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CovApp v1.1

CovApp is an R shiny app that shows gene coverage boxplots for in-house WES data. See ./CovApp/App.R for application code.

coverage-app

Data Sources

CovApp app renders plots using three source files:

  • covtidy.txt lists the percentage coverage above 20X for each gene in each sample.
  • covtidy_genes.txt lists unique genes in covtidy.txt.
  • covtidy_median.txt lists the median percentage coverage above 20X for each gene across all samples.

All three source files are generated by create_covtidy.py, a script that requires *.chanjo_txt files output by the WES pipeline.

Deployment

CovApp is hosted at shinyapps.io.

Contact

Viapath Genome Informatics.