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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/broadSeq.html below:

Bioconductor - broadSeq (development version)

broadSeq

This is the development version of broadSeq; for the stable release version, see broadSeq.

broadSeq : for streamlined exploration of RNA-seq data

Bioconductor version: Development (3.22)

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.

Author: Rishi Das Roy [aut, cre] ORCID: 0000-0002-3276-7279

Maintainer: Rishi Das Roy <rishi.dasroy at gmail.com>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("broadSeq")

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("broadSeq")
Details biocViews Coverage, DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, RNASeq, Sequencing, Software, Transcriptomics Version 1.3.2 In Bioconductor since BioC 3.20 (R-4.4) (0.5 years) License MIT + file LICENSE Depends dplyr, ggpubr, SummarizedExperiment Imports BiocStyle, DELocal, EBSeq(>= 1.38.0), DESeq2(>= 1.38.2), NOISeq, forcats (>= 1.0.0), genefilter, ggplot2, ggplotify, plyr, clusterProfiler(>= 4.8.2), pheatmap, sechm(>= 1.6.0), stringr, purrr (>= 0.3.5), edgeR(>= 3.40.1) System Requirements URL https://github.com/dasroy/broadSeq Bug Reports https://github.com/dasroy/broadSeq/issues See More Package Archives

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

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