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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:
 [1];  [2];  [2];  [3]
  1. Cornell Univ., Ithaca, NY (United States). School of Integrative Plant Science; Max Planck Inst. for Developmental Biology, Tubingen (Germany)
  2. Cornell Univ., Ithaca, NY (United States). School of Integrative Plant Science
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
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:
Journal Article: Published Article
Journal Name:
PLoS ONE
Additional Journal Information:
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, 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, 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, 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, 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},
issn = {1932-6203},
number = 1,
volume = 13,
place = {United States},
year = {2018},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 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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Works referenced in this record:

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    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.