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| CNOGpro-package | CNOGpro - Copy Numbers of Genes in Prokaryotes |
| carsonella | CNV experiment of C. Carsonella ruddy (artificial data) |
| CNOGpro | Set up a new CNOGpro experiment |
| normalizeGC | Normalization of read count data by GC content |
| plotCNOGpro | Plots the results of a 'CNOGpro' experiment |
| printCNOGpro | Prints the results of a 'CNOGpro' experiment |
| runBootstrap | Gene copy numbers with confidence intervals through bootstrapping |
| runHMM | Copy number variation inference through a Hidden Markov Model |
| store | Store the results of a 'CNOGpro' copy number experiment |
| summaryCNOGpro | Summarize the 'CNOGpro' experiment |