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A case study for fagin

This repo contains the code needed to generate the tables and figures used in the synder paper and its supplementary files. And more.

See main fagin page here

Dependencies

CRAN R packages:

  • knitr
  • magrittr
  • rmonad

GitHub R Packages:

  • arendsee/fagin
  • arendsee/synder

The CRAN packages can be installed from an R shell with as so

install.packages("knitr")

and the GitHub packages can be installed with devtools:

library(devtools)
install_github("arendsee/fagin")

Yeast Case Study

All data needed to run this program is available on DataHub. To retrieve this data, first install the data CLI tool by following the instructions available here. Then run the command:

make init

This will download all the input dataset from DataHub and then organize it the way fagin wants.

You can then run the yeast case study with the command:

make run-yeast

Brassicaceae Case Study

To run this study you will need to retrieve the appropriate data, which I will leave as an exercise for the reader.