profileplyr

DOI: 10.18129/B9.bioc.profileplyr    

Visualization and annotation of read signal over genomic ranges with profileplyr

Bioconductor version: Release (3.9)

Quick and straighforward 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>

Citation (from within R, enter citation("profileplyr")):

Installation

To install this package, start R (version "3.6") 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 1.0.1
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
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, EnrichedHeatmap, ComplexHeatmap, grid, circlize, BiocParallel, rtracklayer, GenomeInfoDb
LinkingTo
Suggests BiocStyle, testthat, knitr, rmarkdown, png, Rsamtools, ggplot2
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_1.0.1.tar.gz
Windows Binary profileplyr_1.0.1.zip
Mac OS X 10.11 (El Capitan) profileplyr_1.0.1.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
Old Source Packages for BioC 3.9 Source Archive

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