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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ballgown")
In most cases, you don't need to download the package archive at all.
ballgown
Flexible, isoform-level differential expression analysis
Bioconductor version: 3.0
Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.
Author: Alyssa C. Frazee, Andrew E. Jaffe, Leonardo Collado-Torres, Jeffrey T. Leek
Maintainer: Alyssa Frazee <alyssa.frazee at gmail.com>
Citation (from within R,
enter citation("ballgown")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ballgown")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ballgown")
| HTML | R Script | Flexible isoform-level differential expression analysis with Ballgown |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, Preprocessing, RNASeq, Software, StatisticalMethod |
| Version | 1.0.4 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0.0), methods |
| Imports | GenomicRanges(>= 1.17.25), IRanges(>= 1.99.22), S4Vectors(>= 0.1.2), RColorBrewer, splines, sva, limma, rtracklayer(>= 1.25.13), Biobase(>= 2.25.0), GenomeInfoDb |
| LinkingTo | |
| Suggests | testthat, knitr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | polyester |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ballgown_1.0.4.tar.gz |
| Windows Binary | ballgown_1.0.4.zip |
| Mac OS X 10.6 (Snow Leopard) | ballgown_1.0.4.tgz |
| Mac OS X 10.9 (Mavericks) | ballgown_1.0.4.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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