Package: seqArchRplus 1.5.0

Sarvesh Nikumbh

seqArchRplus: Downstream analyses of promoter sequence architectures and HTML report generation

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.

Authors:Sarvesh Nikumbh [aut, cre, cph]

seqArchRplus_1.5.0.tar.gz
seqArchRplus_1.5.0.zip(r-4.5)seqArchRplus_1.5.0.zip(r-4.4)seqArchRplus_1.5.0.zip(r-4.3)
seqArchRplus_1.5.0.tgz(r-4.4-any)seqArchRplus_1.5.0.tgz(r-4.3-any)
seqArchRplus_1.5.0.tar.gz(r-4.5-noble)seqArchRplus_1.5.0.tar.gz(r-4.4-noble)
seqArchRplus_1.5.0.tgz(r-4.4-emscripten)seqArchRplus_1.5.0.tgz(r-4.3-emscripten)
seqArchRplus.pdf |seqArchRplus.html✨
seqArchRplus/json (API)
NEWS

# Install 'seqArchRplus' in R:

install.packages('seqArchRplus', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/snikumbh/seqarchrplus/issues

On BioConductor:seqArchRplus-1.5.0(bioc 3.20)seqArchRplus-1.4.0(bioc 3.19)

bioconductor-package

15 exports 0.36 score 230 dependencies

Last updated 2 months agofrom:67eccab0ec

Exports:curate_clusters form_combined_panel generate_all_plots generate_html_report handle_tc_from_cage iqw_tpm_plots order_clusters_iqw per_cluster_annotations per_cluster_go_term_enrichments per_cluster_seqlogos per_cluster_strand_dist plot_motif_heatmaps plot_motif_heatmaps2 seqs_acgt_image write_seqArchR_cluster_track_bed

Dependencies:abind AnnotationDbi ape aplot askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob boot broom BSgenome bslib cachem car carData caTools ChIPseeker class cli cluster clusterProfiler codetools colorspace corrplot cowplot cpp11 crayon crosstalk curl cvTools data.table DBI DelayedArray dendextend DEoptimR Deriv digest diptest doBy DOSE downloader dplyr DT EBImage ellipse emmeans enrichplot estimability evaluate factoextra FactoMineR fansi farver fastmap fastmatch fftwtools fgsea flashClust flexmix fontawesome formatR fpc fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggforce ggfun ggimage ggnewscale ggplot2 ggplotify ggpubr ggraph ggrepel ggsci ggseqlogo ggsignif ggtree glue GO.db GOSemSim gplots graphlayouts gridExtra gridGraphics gson gtable gtools HDO.db heatmaps here highr htmltools htmlwidgets httpuv httr igraph IRanges isoband jpeg jquerylib jsonlite KEGGREST kernlab KernSmooth knitr labeling lambda.r later lattice lazyeval leaps lifecycle lme4 locfit magick magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mclust memoise mgcv microbenchmark mime minqa modelr modeltools multcompView munsell mvtnorm nlme nloptr nnet numDeriv openssl patchwork pbkrtest pillar pkgconfig plogr plotrix plyr png polyclip polynom prabclus prettyunits promises purrr quantreg qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppTOML RCurl reshape2 restfulr reticulate Rhtslib rjson rlang rmarkdown robustbase rprojroot Rsamtools RSQLite rstatix rtracklayer S4Arrays S4Vectors sass scales scatterpie scatterplot3d seqArchR seqPattern shadowtext snow SparseArray SparseM stringi stringr SummarizedExperiment survival sys systemfonts tibble tidygraph tidyr tidyselect tidytree tiff tinytex treeio tweenr TxDb.Hsapiens.UCSC.hg19.knownGene UCSC.utils utf8 vctrs viridis viridisLite withr xfun XML XVector yaml yulab.utils zlibbioc

seqArchRplus facilitates downstream analysis of clusters of promoter sequence architectures

Sarvesh Nikumbh

Rendered fromseqArchRplus.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2023-05-05
Started: 2022-04-28

Help page	Topics
Curate clusters from seqArchR result	curate_clusters
Form a combined panel of three plots	form_combined_panel
Generate all plots for a given sample	generate_all_plots
Generate HTML report with scrollable combined panel plots	generate_html_report
Handle writing of tag clusters (TCs) from CAGE experiment to disk as BED files.	handle_tc_from_cage
IQW, TPM plots	iqw_tpm_plots
Order clusters by median or mean interquantile widths	order_clusters_iqw
per_cluster_annotations	per_cluster_annotations
Perform per cluster GO term enrichment analysis	per_cluster_go_term_enrichments
Plot per cluster sequence logos	per_cluster_seqlogos
Visualize as barplots how promoters in each cluster are distributed on different chromosomes and strands	per_cluster_strand_dist
Plot heatmaps of motifs occurring in seqArchR clusters	plot_motif_heatmaps
Plot heatmaps of motifs occurring in seqArchR clusters	plot_motif_heatmaps2
seqArchRplus: A package for downstream analyses of promoter sequence architectures/clusters identified by seqArchR	seqArchRplus
Visualize all sequences as an image	seqs_acgt_image
Write seqArchR cluster information in BED files viewable as browser tracks	write_seqArchR_cluster_track_bed

Package: seqArchRplus 1.5.0

seqArchRplus: Downstream analyses of promoter sequence architectures and HTML report generation

seqArchRplus facilitates downstream analysis of clusters of promoter sequence architectures

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