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)

Documentation

All documentation can be found on CRAN.

A good place to start is the HTSSIP introduction vignette.

The manuscript describing HTSSIP is:

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")

News

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

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("HTSSIP")

1.4.0 by Samuel Barnett, a month 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