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Title: 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) (SC-23)
OSTI Identifier:
1415514
Alternate Identifier(s):
OSTI ID: 1499888
Grant/Contract Number:  
SC0004486; SC0010558
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. doi: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. doi: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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1371/journal.pone.0189616

Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

Figures / Tables:

Fig 1. 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.