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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("BiocCaseStudies")
In most cases, you don't need to download the package archive at all.
BiocCaseStudies
BiocCaseStudies: Support for the Case Studies Monograph
Bioconductor version: 3.0
Software and data to support the case studies.
Author: R. Gentleman, W. Huber, F. Hahne, M. Morgan, S. Falcon
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
Citation (from within R,
enter citation("BiocCaseStudies")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("BiocCaseStudies")
Documentation
| Reference Manual |
Details
| biocViews | Infrastructure, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 2.2 (R-2.7) |
| License | Artistic-2.0 |
| Depends | tools, methods, utils, Biobase |
| Imports | |
| LinkingTo | |
| Suggests | affy(>= 1.17.3), affyPLM(>= 1.15.1), affyQCReport(>= 1.17.0), ALL(>= 1.4.3), annaffy(>= 1.11.1), annotate(>= 1.17.3), AnnotationDbi(>= 1.1.6), apComplex(>= 2.5.0), Biobase(>= 1.17.5), bioDist(>= 1.11.3), biocGraph(>= 1.1.1), biomaRt(>= 1.13.5), CCl4(>= 1.0.6), CLL(>= 1.2.4), Category(>= 2.5.0), class (>= 7.2-38), cluster (>= 1.11.9), convert(>= 1.15.0), gcrma(>= 2.11.1), genefilter(>= 1.17.6), geneplotter(>= 1.17.2), GO.db(>= 2.0.2), GOstats(>= 2.5.0), graph(>= 1.17.4), GSEABase(>= 1.1.13), hgu133a.db(>= 2.0.2), hgu95av2.db, hgu95av2cdf(>= 2.0.0), hgu95av2probe(>= 2.0.0), hopach(>= 1.13.0), KEGG.db(>= 2.0.2), kohonen (>= 2.0.2), lattice (>= 0.17.2), latticeExtra (>= 0.3-1), limma(>= 2.13.1), MASS (>= 7.2-38), MLInterfaces(>= 1.13.17), multtest(>= 1.19.0), org.Hs.eg.db(>= 2.0.2), ppiStats(>= 1.5.4), randomForest (>= 4.5-20), RBGL(>= 1.15.6), RColorBrewer (>= 1.0-2), Rgraphviz(>= 1.17.11), vsn(>= 3.4.0), weaver(>= 1.5.0), xtable (>= 1.5-2), yeastExpData(>= 0.9.11) |
| 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 | BiocCaseStudies_1.28.0.tar.gz |
| Windows Binary | BiocCaseStudies_1.28.0.zip |
| Mac OS X 10.6 (Snow Leopard) | BiocCaseStudies_1.28.0.tgz |
| Mac OS X 10.9 (Mavericks) | BiocCaseStudies_1.28.0.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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