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).


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")
devtools::install_github("nick-youngblut/HTSSIP")

News

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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install.packages("HTSSIP")

1.1.1 by Nicholas Youngblut, 2 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