HTSSIP

NOTE: This repository is not longer maintained. See The buckleylab fork of HTSSIP for the currently maintained version.

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, Nicholas D., Samuel E. Barnett, and Daniel H. Buckley. 2017. “HTSSIP: An R Package for Analysis of High Throughput Sequencing Data from Nucleic Acid Stable Isotope Probing (SIP) Experiments.” bioRxiv. doi:10.1101/166009.

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("nick-youngblut/HTSSIP")