High Throughput Sequencing of Stable Isotope Probing Data Analysis

Functions for analyzing high throughput sequencing stable isotope probing (HTS-SIP) data. Analyses include high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP).

Travis-CI Build Status

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)


All documentation can be found on CRAN.

A good place to start is the HTSSIP introduction vignette.

The manuscript describing HTSSIP is:


See References in the HTSSIP introduction vignette.


To get the current released version from CRAN:


To get the current development version from github:

# install.packages("devtools")


HTSSIP 1.4.0

  • replaced sample data with smaller dataset for storage/memory and processing time constraints
  • updated package requirements to more up-to-data packages

HTSSIP 1.3.2

  • transferred maintainership from NY to SB

HTSSIP 1.3.1

  • added citation information following publication in PLoS ONE

HTSSIP 1.3.0

  • added heavy_SIP() function for conducting historically used SIP analysis methods
  • altered and expanded the permutation methods used for BD_shift()

HTSSIP 1.2.0

  • added permutation test to BD_shift()
  • update function documentation
  • fixed a couple of small bugs

HTSSIP 1.1.1

  • small documentation updates and bug fixes

HTSSIP 1.1.0

  • fixed BD ordination plotting standard evaluation bug

HTSSIP 1.0.3

  • CRAN release

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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1.4.1 by Samuel Barnett, 2 years ago

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

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

Documentation:   PDF Manual  

GPL-2 | file LICENSE license

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

Suggests testthat, knitr, rmarkdown, doParallel

See at CRAN