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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("leeBamViews")
In most cases, you don't need to download the package archive at all.
leeBamViews
leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009
Bioconductor version: 3.0
data from PMID 19096707; prototype for managing multiple NGS samples
Author: VJ Carey <stvjc at channing.harvard.edu>
Maintainer: VJ Carey <stvjc at channing.harvard.edu>
Citation (from within R,
enter citation("leeBamViews")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("leeBamViews")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("leeBamViews")
| R Script | managing multiple NGS samples with bamViews | |
| Reference Manual |
Details
| biocViews | CellBiology, DifferentialExpression, ExperimentData, Genetics, HighThroughputSequencing, RNAseq, RNAseqData |
| Version | 1.1.1 |
| License | Artistic 2.0 |
| Depends | R (>= 2.15.0), Biobase, Rsamtools(>= 0.1.50), BSgenome |
| Imports | GenomicRanges, GenomicAlignments, methods |
| LinkingTo | |
| Suggests | GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR |
| SystemRequirements | |
| Enhances | multicore |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | EDASeq |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | leeBamViews_1.1.1.tar.gz |
| Windows Binary | leeBamViews_1.1.1.zip |
| Mac OS X 10.6 (Snow Leopard) | leeBamViews_1.1.1.tgz |
| Mac OS X 10.9 (Mavericks) | leeBamViews_1.1.1.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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