To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ffpe")
In most cases, you don't need to download the package archive at all.
ffpe
Quality assessment and control for FFPE microarray expression data
Bioconductor version: 2.14
Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).
Author: Levi Waldron
Maintainer: Levi Waldron <levi.waldron at hunter.cuny.edu>
Citation (from within R,
enter citation("ffpe")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ffpe")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ffpe")
| R Script | ffpe package user guide | |
| Reference Manual |
Details
| biocViews | GeneExpression, Microarray, QualityControl, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | GPL (>2) |
| Depends | R (>= 2.10.0), TTR, methods |
| Imports | Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc |
| Suggests | genefilter, ffpeExampleData |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ffpe_1.8.0.tar.gz |
| Windows Binary | ffpe_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ffpe_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | ffpe_1.8.0.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
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