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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("regionReport")
In most cases, you don't need to download the package archive at all.
regionReport
Generate HTML reports for exploring a set of regions
Bioconductor version: 3.0
Generate HTML reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder.
Author: Leonardo Collado-Torres [aut, cre], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Maintainer: Leonardo Collado-Torres <lcollado at jhu.edu>
Citation (from within R,
enter citation("regionReport")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("regionReport")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("regionReport")
| HTML | R Script | Introduction to regionReport |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Coverage, DifferentialExpression, RNASeq, Sequencing, Software, Transcription, Visualization |
| Version | 1.0.5 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | R (>= 3.1.1) |
| Imports | derfinder(>= 1.0.0), derfinderPlot(>= 1.0.0), devtools (>= 1.6), GenomeInfoDb, GenomicRanges, ggbio(>= 1.13.13), ggplot2, grid, gridExtra, IRanges, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), mgcv, RColorBrewer, rmarkdown (>= 0.3.3) |
| LinkingTo | |
| Suggests | biovizBase, Cairo, TxDb.Hsapiens.UCSC.hg19.knownGene |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/lcolladotor/regionReport |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | regionReport_1.0.5.tar.gz |
| Windows Binary | regionReport_1.0.5.zip |
| Mac OS X 10.6 (Snow Leopard) | regionReport_1.0.5.tgz |
| Mac OS X 10.9 (Mavericks) | regionReport_1.0.5.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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