broadSeq

broadSeq : for streamlined exploration of RNA-seq data

Bioconductor version: 3.23 · Package version: 1.6.0

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.

Installation

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

BiocManager::install("broadSeq")

Details

Maintainer	Rishi Das Roy <rishi.dasroy@gmail.com>
Author	Rishi Das Roy [aut, cre] (ORCID: <https://orcid.org/0000-0002-3276-7279>)
License	MIT + file LICENSE
URL	https://github.com/dasroy/broadSeq
Bug Reports	https://github.com/dasroy/broadSeq/issues
Downloads rank	144
Source branch	RELEASE_3_23
biocViews	Coverage, DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, RNASeq, Sequencing, Software, Transcriptomics

Documentation

Using broadSeq to analyze RNA-seq data

Download

Source package

Dependencies

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)

Suggests: knitr, limma (>= 3.54.0), rmarkdown, stats (>= 4.2.2), samr