seqArchRplus

DOI: 10.18129/B9.bioc.seqArchRplus  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see seqArchRplus.

Downstream analyses of promoter sequence architectures and HTML report generation

Bioconductor version: 3.17

seqArchRplus facilitates downstream analyses of promoter sequence architectures/clusters identified by seqArchR (or any other tool/method). With additional available information such as the TPM values and interquantile widths (IQWs) of the CAGE tag clusters, seqArchRplus can order the input promoter clusters by their shape (IQWs), and write the cluster information as browser/IGV track files. Provided visualizations are of two kind: per sample/stage and per cluster visualizations. Those of the first kind include: plot panels for each sample showing per cluster shape, TPM and other score distributions, sequence logos, and peak annotations. The second include per cluster chromosome-wise and strand distributions, motif occurrence heatmaps and GO term enrichments. Additionally, seqArchRplus can also generate HTML reports for easy viewing and comparison of promoter architectures between samples/stages (future).

Author: Sarvesh Nikumbh [aut, cre, cph]

Maintainer: Sarvesh Nikumbh <sarvesh.nikumbh at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("seqArchRplus")

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("seqArchRplus")

 

HTML	R Script	seqArchRplus facilitates downstream analysis of clusters of promoter sequence architectures
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Clustering, GO, MotifAnnotation, ReportWriting, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 4.2), GenomicRanges, IRanges, S4Vectors
Imports	BiocParallel, Biostrings, BSgenome, ChIPseeker, cli, clusterProfiler, cowplot, factoextra, forcats, GenomeInfoDb, ggplot2, graphics, grDevices, gridExtra, heatmaps, methods, RColorBrewer, scales, seqArchR, seqPattern, stats, utils
LinkingTo
Suggests	BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr(>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, rmarkdown (>= 1.12), TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun
SystemRequirements
Enhances
URL	https://github.com/snikumbh/seqArchRplus
BugReports	https://github.com/snikumbh/seqArchRplus/issues
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	seqArchRplus_1.0.0.tar.gz
Windows Binary	seqArchRplus_1.0.0.zip
macOS Binary (x86_64)	seqArchRplus_1.0.0.tgz
macOS Binary (arm64)	seqArchRplus_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/seqArchRplus
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seqArchRplus
Bioc Package Browser	https://code.bioconductor.org/browse/seqArchRplus/
Package Short Url	https://bioconductor.org/packages/seqArchRplus/
Package Downloads Report	Download Stats