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Bioconductor - seqArchRplus

seqArchRplus

This is the released version of seqArchRplus; for the devel version, see seqArchRplus.

Downstream analyses of promoter sequence architectures and HTML report generation

Bioconductor version: Release (3.21)

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] ORCID: 0000-0003-3163-4447

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

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

To install this package, start R (version "4.5") 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 1.8.0 In Bioconductor since BioC 3.17 (R-4.3) (2 years) 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 Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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