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seqArchRplus

Downstream analyses of promoter sequence architectures and HTML report generation


Bioconductor version: Release (3.18)

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.

Author: Sarvesh Nikumbh [aut, cre, cph]

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

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

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

Details

biocViews Annotation, Clustering, GO, MotifAnnotation, ReportWriting, Software, Visualization
Version 1.2.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2), GenomicRanges, IRanges, S4Vectors
Imports BiocParallel, Biostrings, BSgenome, ChIPseeker, cli, clusterProfiler, cowplot, factoextra, GenomeInfoDb, ggplot2, ggimage, graphics, grDevices, gridExtra, heatmaps, magick, methods, RColorBrewer, scales, seqArchR, seqPattern, stats, utils
System Requirements
URL https://github.com/snikumbh/seqArchRplus
Bug Reports https://github.com/snikumbh/seqArchRplus/issues
See More
Suggests BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr(>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>= 1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun
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Package Archives

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

Source Package seqArchRplus_1.2.0.tar.gz
Windows Binary seqArchRplus_1.2.0.zip (64-bit only)
macOS Binary (x86_64) seqArchRplus_1.2.0.tgz
macOS Binary (arm64) seqArchRplus_1.2.0.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/
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