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).
| Version: | 1.4.1 |
| Depends: | R (≥ 3.4.0) |
| Imports: | igraph (≥ 1.1.2), ape (≥ 4.1), magrittr (≥ 1.5), stringr (≥ 1.2.0), plyr (≥ 1.8.4), dplyr (≥ 0.7.4), tidyr (≥ 0.7.2), ggplot2 (≥ 2.2.1), vegan (≥ 2.4.0), DESeq2 (≥ 1.16.1), phyloseq (≥ 1.20.0), coenocliner (≥ 0.2.2), lazyeval (≥ 0.2.0) |
| Suggests: | testthat, knitr, rmarkdown, doParallel |
| Published: | 2019-09-13 |
| DOI: | 10.32614/CRAN.package.HTSSIP |
| Author: | Nicholas Youngblut [aut], Samuel Barnett [cre, ctb] |
| Maintainer: | Samuel Barnett <seb369 at cornell.edu> |
| License: | GPL-2 | file LICENSE |
| NeedsCompilation: | no |
| Citation: | HTSSIP citation info |
| Materials: | README NEWS |
| CRAN checks: | HTSSIP results [issues need fixing before 2024-11-18] |
| Reference manual: | HTSSIP.pdf |
| Vignettes: |
BD shifts HTSSIP introduction HTS-SIP data simulation MW-HR-SIP Beta diversity ordinations heavy-SIP q-SIP Quantifying isotope incorporation |
| Package source: | HTSSIP_1.4.1.tar.gz |
| Windows binaries: | r-devel: HTSSIP_1.4.1.zip, r-release: HTSSIP_1.4.1.zip, r-oldrel: HTSSIP_1.4.1.zip |
| macOS binaries: | r-release (arm64): HTSSIP_1.4.1.tgz, r-oldrel (arm64): HTSSIP_1.4.1.tgz, r-release (x86_64): HTSSIP_1.4.1.tgz, r-oldrel (x86_64): HTSSIP_1.4.1.tgz |
| Old sources: | HTSSIP archive |
| Reverse imports: | SIPmg |
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