micropan: an R-package for microbial pan-genomics View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-12

AUTHORS

Lars Snipen, Kristian Hovde Liland

ABSTRACT

BACKGROUND: A pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species. Due to the extensive within-species diversity in the microbial world, the pan-genome is often many times larger than a single genome. Studies of pan-genomes have become popular due to the easy access to whole-genome sequence data for prokaryotes. A pan-genome study reveals species diversity and gene families that may be of special interest, e.g because of their role in bacterial survival or their ability to discriminate strains. RESULTS: We present an R package for the study of prokaryotic pan-genomes. The R computing environment harbors endless possibilities with respect to statistical analyses and graphics. External free software is used for the heavy computations involved, and the R package provides functions for building a computational pipeline. CONCLUSIONS: We demonstrate parts of the package on a data set for the gram positive bacterium Enterococcus faecalis. The package is free to download and install from The Comprehensive R Archive Network. More... »

PAGES

79

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12859-015-0517-0

DOI

http://dx.doi.org/10.1186/s12859-015-0517-0

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1008563065

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25888166


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