profileplyr
Visualization and annotation of read signal over genomic ranges with profileplyr
Bioconductor version: Release (3.17)
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>
citation("profileplyr")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("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")| Visualization and annotation of read signal over genomic ranges with profileplyr | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, ChipOnChip, Coverage, DataImport, Sequencing, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (4.5 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, tiff, Rsamtools |
| Linking To | |
| Suggests | BiocStyle, testthat, knitr, rmarkdown, png, Cairo |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | DiffBind |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | profileplyr_1.16.0.tar.gz |
| Windows Binary | profileplyr_1.16.0.zip |
| macOS Binary (x86_64) | profileplyr_1.16.0.tgz |
| macOS Binary (arm64) | profileplyr_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/profileplyr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/profileplyr |
| Bioc Package Browser | https://code.bioconductor.org/browse/profileplyr/ |
| Package Short Url | https://bioconductor.org/packages/profileplyr/ |
| Package Downloads Report | Download Stats |