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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("phyloseq")
In most cases, you don't need to download the package archive at all.
phyloseq
Handling and analysis of high-throughput microbiome census data.
Bioconductor version: 2.14
phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.
Author: Paul J. McMurdie <mcmurdie at stanford.edu>, Susan Holmes <susan at stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain
Maintainer: Paul J. McMurdie <mcmurdie at stanford.edu>
Citation (from within R,
enter citation("phyloseq")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("phyloseq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("phyloseq")
| HTML | R Script | phyloseq analysis vignette |
| HTML | R Script | phyloseq and DESeq2 on Colorectal Cancer Data |
| HTML | R Script | phyloseq basics vignette |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, Clustering, GeneticVariability, HighThroughputSequencing, MultipleComparisons, QualityControl, Software |
| Version | 1.8.2 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | AGPL-3 |
| Depends | R (>= 3.0.0) |
| Imports | ade4 (>= 1.6.2), ape (>= 3.1.1), biom (>= 0.3.9), Biostrings(>= 2.28.0), cluster (>= 1.14.4), data.table (>= 1.9.2), DESeq2(>= 1.4.0), foreach (>= 1.4.2), ggplot2 (>= 1.0.0), igraph (>= 0.6.5.2), methods (>= 3.0.0), multtest(>= 2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.2.3), vegan (>= 2.0.10) |
| Suggests | genefilter(>= 1.42.0), testthat (>= 0.7.1), knitr (>= 1.3) |
| System Requirements | |
| URL | http://dx.plos.org/10.1371/journal.pone.0061217 |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | phyloseq_1.8.2.tar.gz |
| Windows Binary | phyloseq_1.8.2.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | phyloseq_1.8.2.tgz |
| Mac OS X 10.9 (Mavericks) | phyloseq_1.8.2.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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