HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

Perform HTS-SIP analyses such as high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP). More information on HR-SIP, MW-HR-SIP, and q-SIP can be found in: 1) Pepe-Ranney, Charles, Ashley N. Campbell, Chantal N. Koechli, Sean Berthrong, and Daniel H. Buckley. 2016. "Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil." Terrestrial Microbiology, 703. <doi:10.3389/fmicb.2016.00703> 2) Youngblut, Nicholas D., and Daniel H. Buckley. "Evaluating the Accuracy of DNA Stable Isotope Probing". in prep. 3) Hungate, Bruce A., Rebecca L. Mau, Egbert Schwartz, J. Gregory Caporaso, Paul Dijkstra, Natasja van Gestel, Benjamin J. Koch, et al. 2015. "Quantitative Microbial Ecology Through Stable Isotope Probing." Applied and Environmental Microbiology, August, AEM.02280-15. <doi:10.1128/AEM.02280-15>

Version: 1.0.3
Depends: R (≥ 3.1.2)
Imports: magrittr (≥ 1.5), stringr (≥ 1.0.0), plyr (≥ 1.8.4), dplyr (≥ 0.5.0), tidyr (≥ 0.5.1), ggplot2 (≥ 2.1.0), DESeq2 (≥ 1.10.1), phyloseq (≥ 1.14.0), coenocliner (≥ 0.2.2), lazyeval (≥ 0.2.0)
Suggests: testthat, knitr, rmarkdown, doParallel
Published: 2016-11-01
Author: Nicholas Youngblut [aut, cre], Samuel Barnett [ctb]
Maintainer: Nicholas Youngblut <nyoungb2 at gmail.com>
License: GPL-2 | file LICENSE
NeedsCompilation: no
Citation: HTSSIP citation info
Materials: README NEWS
CRAN checks: HTSSIP results

Downloads:

Reference manual: HTSSIP.pdf
Vignettes: BD shifts
HTSSIP introduction
HTS-SIP data simulation
MW-HR-SIP
Beta diversity ordinations
q-SIP
Quantifying isotope incorporation
Package source: HTSSIP_1.0.3.tar.gz
Windows binaries: r-devel: HTSSIP_1.0.3.zip, r-release: HTSSIP_1.0.3.zip, r-oldrel: HTSSIP_1.0.3.zip
OS X El Capitan binaries: r-release: not available
OS X Mavericks binaries: r-oldrel: HTSSIP_1.0.3.tgz

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