profileplyr

DOI: 10.18129/B9.bioc.profileplyr    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see profileplyr.

Visualization and annotation of read signal over genomic ranges with profileplyr

Bioconductor version: 3.13

Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.

Author: Tom Carroll and Doug Barrows

Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Doug Barrows <doug.barrows at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("profileplyr")

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("profileplyr")

 

HTML	R Script	Visualization and annotation of read signal over genomic ranges with profileplyr
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, ChipOnChip, Coverage, DataImport, Sequencing, Software
Version	1.8.1
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	GPL (>= 3)
Depends	R (>= 3.6), BiocGenerics, SummarizedExperiment
Imports	GenomicRanges, stats, soGGi, methods, utils, S4Vectors, R.utils, dplyr, magrittr, tidyr, IRanges, rjson, ChIPseeker, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Hs.eg.db, org.Mm.eg.db, rGREAT, pheatmap, ggplot2, EnrichedHeatmap, ComplexHeatmap, grid, circlize, BiocParallel, rtracklayer, GenomeInfoDb, grDevices, rlang, Cairo, tiff, Rsamtools
LinkingTo
Suggests	BiocStyle, testthat, knitr, rmarkdown, png
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	profileplyr_1.8.1.tar.gz
Windows Binary	profileplyr_1.8.1.zip
macOS 10.13 (High Sierra)	profileplyr_1.8.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/profileplyr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/profileplyr
Package Short Url	https://bioconductor.org/packages/profileplyr/
Package Downloads Report	Download Stats