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Downstream analyses of promoter sequence architectures and HTML report generation

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Annotation, Clustering, GO, MotifAnnotation, ReportWriting, Software, Visualization
Version 1.4.0
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
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Suggests BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr(>= 2.0.2), covr, knitr (>= 1.22),, pdftools, rmarkdown (>= 1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun
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Source Package seqArchRplus_1.4.0.tar.gz
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macOS Binary (x86_64) seqArchRplus_1.4.0.tgz
macOS Binary (arm64) seqArchRplus_1.4.0.tgz
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