High Throughput Sequencing of Stable Isotope Probing Data Analysis

Perform HTS-SIP analyses such as high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP). More information on HR-SIP, MW-HR-SIP, and q-SIP can be found in: 1) Pepe-Ranney, Charles, Ashley N. Campbell, Chantal N. Koechli, Sean Berthrong, and Daniel H. Buckley. 2016. "Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil." Terrestrial Microbiology, 703. 2) Youngblut, Nicholas D., and Daniel H. Buckley. "Evaluating the Accuracy of DNA Stable Isotope Probing". in prep. 3) Hungate, Bruce A., Rebecca L. Mau, Egbert Schwartz, J. Gregory Caporaso, Paul Dijkstra, Natasja van Gestel, Benjamin J. Koch, et al. 2015. "Quantitative Microbial Ecology Through Stable Isotope Probing." Applied and Environmental Microbiology, August, AEM.02280-15.

HTSSIP is an R package for analyzing high throughput sequence data from nucleotide stable isotope probing (DNA- & RNA-SIP) experiments.

  • Identifying community-level isotope incorporatation

    • Ordinations of gradient fraction communities
    • Beta diversity of overlapping gradient fractions
  • Identifying isotope incorporators

    • High resolution stable isotope probing (HR-SIP)
    • Multiple window high resolution stable isotope probing (MW-HR-SIP)
    • Quantitative stable isotope probing (q-SIP)

A good place to start is the HTSSIP introduction vignette.

See References in the HTSSIP introduction vignette.

To get the current released version from CRAN:

install.packages("HTSSIP")  # sorry: the package is not yet on CRAN

To get the current development version from github:

# install.packages("devtools")


HTSSIP 1.0.2

  • Fixed CRAN namesspace warnings/notes
  • Reduced run time of examples, tests, and vignettes

HTSSIP 1.0.1

  • Reduced run time of examples, tests, and vignettes

HTSSIP 1.0.0

  • Examples for exported functions.
  • Tests covering all exported functions.
  • Vignettes for each category of analyses available with the package.

Reference manual

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1.0.3 by Nicholas Youngblut, 5 months ago

Browse source code at https://github.com/cran/HTSSIP

Authors: Nicholas Youngblut [aut, cre], Samuel Barnett [ctb]

Documentation:   PDF Manual  

GPL-2 | file LICENSE license

Imports magrittr, stringr, plyr, dplyr, tidyr, ggplot2, DESeq2, phyloseq, coenocliner, lazyeval

Suggests testthat, knitr, rmarkdown, doParallel

See at CRAN