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:
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 in the HTSSIP introduction vignette.
To get the current released version from CRAN:
To get the current development version from github:
# install.packages("devtools") devtools::install_github("buckleylab/HTSSIP")