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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("metagenomeSeq")
In most cases, you don't need to download the package archive at all.
metagenomeSeq
Statistical analysis for sparse high-throughput sequencing
Bioconductor version: 3.0
metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.
Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Maintainer: Joseph N. Paulson <jpaulson at umiacs.umd.edu>
Citation (from within R,
enter citation("metagenomeSeq")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("metagenomeSeq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("metagenomeSeq")
| R Script | metagenomeSeq: statistical analysis for sparse high-throughput sequencing | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, Metagenomics, Software, Visualization |
| Version | 1.8.3 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0), Biobase, limma, methods, interactiveDisplay(>= 1.3.24), RColorBrewer |
| Imports | parallel, matrixStats, gplots |
| LinkingTo | |
| Suggests | annotate, BiocGenerics, biom, knitr, gss, RUnit, vegan |
| SystemRequirements | |
| Enhances | |
| URL | http://cbcb.umd.edu/software/metagenomeSeq |
| Depends On Me | msd16s |
| Imports Me | |
| Suggests Me | interactiveDisplay |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | metagenomeSeq_1.8.3.tar.gz |
| Windows Binary | metagenomeSeq_1.8.3.zip |
| Mac OS X 10.6 (Snow Leopard) | metagenomeSeq_1.8.3.tgz |
| Mac OS X 10.9 (Mavericks) | metagenomeSeq_1.8.3.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
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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