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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ampliQueso")
In most cases, you don't need to download the package archive at all.
ampliQueso
Analysis of amplicon enrichment panels
Bioconductor version: 2.14
The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq
Author: Alicja Szabelska <alicja.szabelska at up.poznan.pl>; Marek Wiewiorka <marek.wiewiorka at gmail.com>; Michal Okoniewski <michal at fgcz.ethz.ch>
Maintainer: Michal Okoniewski <michal at fgcz.ethz.ch>
Citation (from within R,
enter citation("ampliQueso")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ampliQueso")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ampliQueso")
| R Script | ampliQueso primer | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | GPL-2 |
| Depends | R (>= 2.15.0), rnaSeqMap(>= 2.17.1), knitr, rgl, ggplot2, gplots, parallel, doParallel, foreach, VariantAnnotation, genefilter, statmod, xtable |
| Imports | edgeR, DESeq, samr |
| Suggests | |
| 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 | ampliQueso_1.2.0.tar.gz |
| Windows Binary | ampliQueso_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ampliQueso_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | ampliQueso_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
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