regionReport
This is the released version of regionReport; for the devel version, see regionReport.
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Bioconductor version: Release (3.23)
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 <lcolladotor at gmail.com>
citation("regionReport")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, OleÅ AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115â121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| Example report using bumphunter results | HTML | R Script |
| Introduction to regionReport | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DifferentialExpression, DifferentialMethylation, DifferentialPeakCalling, ImmunoOncology, QualityControl, RNASeq, ReportWriting, Sequencing, Software, Transcription, Visualization |
| Version | 1.46.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2) |
| Imports | BiocStyle(>= 2.5.19), derfinder(>= 1.25.3), DEFormats, DESeq2, Seqinfo, GenomeInfoDb, GenomicRanges, knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils |
| System Requirements | |
| URL | https://github.com/leekgroup/regionReport |
| Bug Reports | https://support.bioconductor.org/t/regionReport/ |
See More
| Suggests | BiocManager, biovizBase, bumphunter(>= 1.7.6), derfinderPlot(>= 1.29.1), sessioninfo, DT, edgeR, ggbio(>= 1.35.2), 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_1.46.0.tar.gz |
| Windows Binary (x86_64) | regionReport_1.46.0.zip |
| macOS Binary (big-sur-x86_64) | regionReport_1.46.0.tgz |
| macOS Binary (sonoma-arm64) | regionReport_1.46.0.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 |