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ReScience Ten Year Reproducibility Challenge

DOI

This repository is my contribution to the ReScience Ten Years Reproducibility Challenge.

Broman KW (2020) Reproducibility report: Identifying essential genes by mutagenesis. ReScience C 6 (1): #12 doi:10.5281/zenodo.3959516

I sought 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 PubMed pdf (260k) R/negenes doi

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:

Dependencies

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

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

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

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