regionReport
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see regionReport.
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Bioconductor version: 3.7
Generate HTML or PDF 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. You can also create reports for DESeq2 or edgeR results.
Author: Leonardo Collado-Torres [aut, cre], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Maintainer: Leonardo Collado-Torres <lcollado at jhu.edu>
citation("regionReport")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("regionReport")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("regionReport")| Basic genomic regions exploration | HTML | R Script |
| Example report using bumphunter results | HTML | R Script |
| Introduction to regionReport | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DifferentialExpression, DifferentialMethylation, DifferentialPeakCalling, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization |
| Version | 1.14.3 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2) |
| Imports | BiocStyle(>= 2.5.19), derfinder(>= 1.1.0), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/leekgroup/regionReport |
| Bug Reports | https://support.bioconductor.org/t/regionReport/ |
See More
| Suggests | biovizBase, bumphunter(>= 1.7.6), derfinderPlot(>= 1.3.2), devtools (>= 1.6), DT, DESeq, edgeR, ggbio(>= 1.13.13), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | recountWorkflow |
| Suggests Me | recount |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | regionReport_1.14.3.tar.gz |
| Windows Binary | regionReport_1.14.3.zip |
| Mac OS X 10.11 (El Capitan) | regionReport_1.14.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/regionReport |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/regionReport |
| Bioc Package Browser | https://code.bioconductor.org/browse/regionReport/ |
| Package Short Url | https://bioconductor.org/packages/regionReport/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |