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README.md

README.md

README

The field of microbiology has experienced significant growth due to transformative advances in technology and the influx of scientists driven by a curiosity to understand how microbes sustain myriad biochemical processes that maintain the Earth. With this explosion in scientific output, a significant bottleneck has been the ability to rapidly disseminate new knowledge to peers and the public. Preprints have emerged as a tool that a growing number of microbiologists are using to overcome this bottleneck. Posting preprints can help to transparently recruit a more diverse pool of reviewers prior to submitting to a journal for formal peer-review. Although use of preprints is still limited in the biological sciences, early indications are that preprints are a robust tool that can complement and enhance peer-reviewed publications. As publishing moves to embrace advances in internet technology, there are many opportunities for preprints and peer-reviewed journals to coexist in the same ecosystem.

Dependencies and locations

  • GNU bash (v.4.1.2)
  • Gnu Make (v.3.81) should be located in the user's PATH
  • R (v. 3.3.2) should be located in the user's PATH
  • The following R packages should be installed:
    • cowplot (v.0.6.9990)
    • dplyr (v.0.5.0)
    • ggplot2 (v.2.1.0.9001)
    • httr (v.1.2.1)
    • RCurl (v.1.95-4.8),
    • rentrez (v.1.0.4)
    • RJSONIO (v.1.3-0)
    • rvest (v.0.3.2)
    • sportcolors (v.0.0.1)
    • tidyr (v.0.6.0)
install.packages(c("cowplot", "dplyr", "ggplot2", "httr", "RCurl", "rentrez", "RJSONIO", "rvest",
									"sportcolors", "tidyr"))

Running analysis

git clone https://github.com/SchlossLab/Schloss_PrePrints_mBio_2017.git
make write.paper