An R package for analyzing high throughput sequence stable isotope probing data
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README.md

HTSSIP

Travis-CI Build Status

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

Available analyzes

  • 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)

Documentation

All documentation can be found on CRAN.

A good place to start is the HTSSIP introduction vignette.

The manuscript describing HTSSIP is:

Youngblut ND, Barnett SE, Buckley DH (2018) HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments. PLoS ONE 13(1): e0189616. https://doi.org/10.1371/journal.pone.0189616

References

See References in the HTSSIP introduction vignette.

Installation

To get the current released version from CRAN:

install.packages("HTSSIP") 

To get the current development version from github:

# install.packages("devtools")
devtools::install_github("buckleylab/HTSSIP")