Package: broadSeq 1.7.0

Rishi Das Roy

broadSeq: broadSeq : for streamlined exploration of RNA-seq data

This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.

Authors:Rishi Das Roy [aut, cre]

broadSeq_1.7.0.tar.gz
broadSeq_1.7.0.zip(r-4.7)broadSeq_1.7.0.zip(r-4.6)broadSeq_1.7.0.zip(r-4.5)
broadSeq_1.7.0.tgz(r-4.6-any)broadSeq_1.7.0.tgz(r-4.5-any)
broadSeq_1.7.0.tar.gz(r-4.7-any)broadSeq_1.7.0.tar.gz(r-4.6-any)
broadSeq_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
broadSeq/json (API)

# Install 'broadSeq' in R:

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

Bug tracker:https://github.com/dasroy/broadseq/issues

On BioConductor:broadSeq-1.7.0(bioc 3.24)broadSeq-1.6.0(bioc 3.23)

geneexpression differentialexpression rnaseq transcriptomics sequencing coverage genesetenrichment go

5.35 score 9 stars 8 scripts 25 exports 230 dependencies

Last updated from:4cc0a21766. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	271
linux-devel-x86_64	WARNING	485
source / vignettes	OK	402
linux-release-x86_64	WARNING	520
macos-release-arm64	WARNING	281
macos-oldrel-arm64	WARNING	243
windows-devel	WARNING	352
windows-release	WARNING	365
windows-oldrel	WARNING	352
wasm-release	OK	253

Exports:assay_plot biplotAnyPC combinedEnrichment genes_plot getFeatureLoadRanking normalizeEdgerCPM plot_MDS plotAnyPC plotHeatmapCluster prcompTidy round_df sampleAssay_plot transformDESeq2 use_DELocal use_deseq2 use_EBSeq use_edgeR use_edgeR_exact use_edgeR_GLM use_limma use_limma_trend use_limma_voom use_multDE use_NOIseq volcanoPlot

Dependencies:abind aisdk annotate AnnotationDbi ape aplot askpass backports base64enc BH Biobase BiocGenerics BiocManager BiocParallel BiocStyle Biostrings bit bit64 bitops blob blockmodeling bookdown boot brio broom bslib ca cachem callr car carData caTools circlize cli clue cluster clusterProfiler codetools colorspace ComplexHeatmap corrplot cowplot cpp11 crayon curl DBI DelayedArray DELocal Deriv desc DESeq2 diffobj digest doBy doParallel DOSE dplyr EBSeq edgeR enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver forcats foreach forecast formatR Formula fracdiff fs futile.logger futile.options gclus gdtools genefilter generics GenomicRanges GetoptLong ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif ggtangle ggtree GlobalOptions glue GO.db GOSemSim gplots gridExtra gridGraphics gson gtable gtools highr htmltools htmlwidgets httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lazyeval lifecycle limma lme4 lmtest locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr nlme nloptr nnet NOISeq numDeriv openssl otel patchwork pbkrtest permute pheatmap pillar pkgbuild pkgconfig pkgload plyr png polyclip polynom praise processx ps purrr qap quantreg qvalue R6 randomcoloR rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas registry reshape2 rjson rlang rmarkdown rprojroot RSQLite rstatix Rtsne S4Arrays S4Vectors S7 sass scales scatterpie sechm Seqinfo seriation shape snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys systemfonts testthat tibble tidydr tidyr tidyselect tidytree timeDate tinytex treeio TSP tweenr urca utf8 V8 vctrs vegan viridisLite waldo withr xfun XML xtable XVector yaml yulab.utils zoo

Using broadSeq to analyze RNA-seq data

Rendered frombroadSeq.Rmdusingknitr::rmarkdown

Last update: 2025-06-25
Started: 2024-03-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
broadSeq : for streamlined exploration of RNA-seq data	broadSeq-package broadSeq
Provides GO gene set enrichment and over-representation analysis	combinedEnrichment
Expression of multiple genes/features from a single assay as boxplot (or added dotplot)	assay_plot genes_plot
Use of edgeR package to normalize count data	normalizeEdgerCPM
Classical multidimensional scaling	plot_MDS
Plot clustered heatmaps	plotHeatmapCluster
Perform Principal Components Analysis	biplotAnyPC getFeatureLoadRanking plotAnyPC prcompTidy
Applies round function only on numeric columns of a data.frame.	round_df
Useful to visualize distribution of assay values for each sample. Plots 'boxplot' of any assay for each sample. Aesthetic can be added from colData.	sampleAssay_plot
Transform SummarizedExperiment with DESeq2 package	transformDESeq2
To use SummarizedExperiment with package DELocal	use_DELocal
To use SummarizedExperiment with package DESeq2	use_deseq2
To use SummarizedExperiment with package EBSeq	use_EBSeq
To use SummarizedExperiment with package edgeR	use_edgeR use_edgeR_exact use_edgeR_GLM
To use SummarizedExperiment with package limma	use_limma use_limma_trend use_limma_voom
To identify differentially expressed genes by multiple methods	use_multDE
Differential expression method for NOISeq	use_NOIseq
To use SummarizedExperiment with package samr	use_SAMseq
Volcano plot with formatted x and y axis label.	volcanoPlot