karthik / Paper_ReScience2020

Paper for the ReScience 10 year reproducibility challenge, reproducing Lamichhane et al (2003).

ReScience Ten Year Reproducibility Challenge

This repository is my contribution to the ReScience Ten Years Reproducibility Challenge. I'm seeking to reproduce the following paper.

Lamichhane G, Zignol M, Blades NJ, Geiman DE, Dougherty A, Broman KW, Bishai WR (2003) A post-genomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis. Proc Natl Acad Sci USA 100:7213-7218

A snapshot of my original project directory for my work related to that paper is in a separate repository on github.

The primary software is the R/negenes package for R, available on github and CRAN.

In this repository:

• negenes/ contains the R/negenes package, version 1.0-12 (2019-08-05).

• original/ contains a subset of the original project directory. Much of the material that was not used for the paper was deleted, as were intermediate results (.RData files).

• talk/ contains a subset of the repository for slides for a 2002 talk on the work; deleted the figures, slides PDF, and a big .RData file. The key thing here is talk/R/circlefig.R which was used to create Figure 1b (of the circular genome).

• reproduction/ contains my reproduction of the analysis, as an R Markdown document. The compiled document can be viewed on the web.

• article/ contains the article about the reproduction effort. The article PDF can be viewed on the web.

Dependencies

The reproduction of the analysis, in reproduction, relies on the following tools:

• R

• R packages: negenes, rmarkdown, devtools, R.utils, xtable, readxl, gt

  Install the first four with install.packages().

  install.packages(c("negenes", "rmarkdown", "devtools", "R.utils", "xtable", "readxl", "broman"))

  Then install gt with devtools::install_github().

  devtools::install_github("rstudio/gt")

• Perl

• Pandoc (most easily installed by installing RStudio Desktop)

• GNU Make

License

This is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3