HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments
Abstract
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.
- Authors:
- Publication Date:
- Research Org.:
- Cornell Univ., Ithaca, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1415514
- Alternate Identifier(s):
- OSTI ID: 1499888; OSTI ID: 1864328
- Grant/Contract Number:
- SC0004486; SC0010558; SC0016364
- Resource Type:
- Published Article
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Name: PLoS ONE Journal Volume: 13 Journal Issue: 1; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING
Citation Formats
Youngblut, Nicholas D., Barnett, Samuel E., Buckley, Daniel H., and Pan, ed., Chongle. HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments. United States: N. p., 2018.
Web. doi:10.1371/journal.pone.0189616.
Youngblut, Nicholas D., Barnett, Samuel E., Buckley, Daniel H., & Pan, ed., Chongle. HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments. United States. https://doi.org/10.1371/journal.pone.0189616
Youngblut, Nicholas D., Barnett, Samuel E., Buckley, Daniel H., and Pan, ed., Chongle. Wed .
"HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments". United States. https://doi.org/10.1371/journal.pone.0189616.
@article{osti_1415514,
title = {HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments},
author = {Youngblut, Nicholas D. and Barnett, Samuel E. and Buckley, Daniel H. and Pan, ed., Chongle},
abstractNote = {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.},
doi = {10.1371/journal.pone.0189616},
journal = {PLoS ONE},
number = 1,
volume = 13,
place = {United States},
year = {2018},
month = {1}
}
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https://doi.org/10.1371/journal.pone.0189616
https://doi.org/10.1371/journal.pone.0189616
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Cited by: 4 works
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Figures / Tables:
Fig 1. : A diagram depicting the possible HTS-SIP analyses available in the HTSSIP R package. The R functions to conduct each workflow step are italicized, and the figure references refer to example data produced by these workflow steps.
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Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.