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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("metaseqR")
In most cases, you don't need to download the package archive at all.
metaseqR
metaseqR: an R package for the analysis and result reporting of RNA-Seq gene expression data using multiple statistical algorithms.
Bioconductor version: 2.14
Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.
Author: Panagiotis Moulos <moulos at fleming.gr>
Maintainer: Panagiotis Moulos <moulos at fleming.gr>
Citation (from within R,
enter citation("metaseqR")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("metaseqR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("metaseqR")
| R Script | RNA-Seq data analysis using mulitple statistical algorithms with metaseqR | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, GeneExpression, Normalization, Preprocessing, QualityControl, RNASeq, ReportWriting, Software, WorkflowStep |
| Version | 1.2.3 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | GPL (>= 3) |
| Depends | R (>= 2.13.0), EDASeq, DESeq, limma, qvalue |
| Imports | edgeR, NOISeq, baySeq, NBPSeq, biomaRt, utils, gplots, corrplot, vsn, brew, rjson, log4r |
| Suggests | BiocGenerics, GenomicRanges, rtracklayer, Rsamtools, MADAM, survcomp, VennDiagram, knitr, zoo, RUnit |
| System Requirements | |
| URL | http://www.fleming.gr |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | metaseqR_1.2.3.tar.gz |
| Windows Binary | metaseqR_1.2.3.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | metaseqR_1.2.3.tgz |
| Mac OS X 10.9 (Mavericks) | metaseqR_1.2.3.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
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