HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

Journal Article · Wed Jan 03 00:00:00 EST 2018 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0189616· OSTI ID:1415514

Youngblut, Nicholas D.; Barnett, Samuel E.; Buckley, Daniel H.; Pan, ed., Chongle

Combining high throughput sequencing with stable isotope probing (HTS-SIP) is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa. However, accurately mapping metabolic processes to taxa is complex and challenging. Multiple HTS-SIP data analysis methods have been developed, including high-resolution stable isotope probing (HR-SIP), multi-window high-resolution stable isotope probing (MW-HR-SIP), quantitative stable isotope probing (qSIP), and ΔBD. Currently, there is no publicly available software designed specifically for analyzing HTS-SIP data. To address this shortfall, we have developed the HTSSIP R package, an open-source, cross-platform toolset for conducting HTS-SIP analyses in a straightforward and easily reproducible manner. The HTSSIP package, along with full documentation and examples, is available from CRAN at https://cran.r-project.org/web/packages/HTSSIP/index.html and Github at https://github.com/buckleylab/HTSSIP.

• Research Organization: Cornell Univ., Ithaca, NY (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: SC0004486; SC0010558; SC0016364
• OSTI ID: 1415514
• Alternate ID(s): OSTI ID: 1499888; OSTI ID: 1864328
• Journal Information: PLoS ONE, Journal Name: PLoS ONE Vol. 13 Journal Issue: 1; ISSN 1932-6203
• Publisher: Public Library of Science
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING