To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ELBOW")
In most cases, you don't need to download the package archive at all.
ELBOW
ELBOW - Evaluating foLd change By the lOgit Way
Bioconductor version: 3.0
Elbow an improved fold change test that uses cluster analysis and pattern recognition to set cut off limits that are derived directly from intrareplicate variance without assuming a normal distribution for as few as 2 biological replicates. Elbow also provides the same consistency as fold testing in cross platform analysis. Elbow has lower false positive and false negative rates than standard fold testing when both are evaluated using T testing and Statistical Analysis of Microarray using 12 replicates (six replicates each for initial and final conditions). Elbow provides a null value based on initial condition replicates and gives error bounds for results to allow better evaluation of significance.
Author: Xiangli Zhang, Natalie Bjorklund, Graham Alvare, Tom Ryzdak, Richard Sparling, Brian Fristensky
Maintainer: Graham Alvare <alvare at cc.umanitoba.ca>, Xiangli Zhang <zhangju at cc.umanitoba.ca>
Citation (from within R,
enter citation("ELBOW")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ELBOW")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ELBOW")
| R Script | Using ELBOW --- the definitive ELBOW tutorial | |
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | GeneExpression, Microarray, MultiChannel, OneChannel, RNASeq, Sequencing, Software, Technology, TwoChannel |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | file LICENSE |
| Depends | R (>= 2.15.0) |
| Imports | |
| LinkingTo | |
| Suggests | DESeq, GEOquery, limma, simpleaffy, affyPLM, RColorBrewer |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ELBOW_1.2.0.tar.gz |
| Windows Binary | ELBOW_1.2.0.zip |
| Mac OS X 10.6 (Snow Leopard) | ELBOW_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | ELBOW_1.2.0.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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