broadSeq
broadSeq : for streamlined exploration of RNA-seq data
Bioconductor version: Release (3.20)
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] 
Maintainer: Rishi Das Roy <rishi.dasroy at gmail.com>
citation("broadSeq")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")| Using broadSeq to analyze RNA-seq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, RNASeq, Sequencing, Software, Transcriptomics |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| 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
| Suggests | knitr, limma(>= 3.54.0), rmarkdown, stats (>= 4.2.2), samr |
| 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.
| Source Package | broadSeq_1.0.0.tar.gz |
| Windows Binary (x86_64) | broadSeq_1.0.0.zip (64-bit only) |
| macOS Binary (x86_64) | broadSeq_1.0.0.tgz |
| macOS Binary (arm64) | broadSeq_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/broadSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/broadSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/broadSeq/ |
| Package Short Url | https://bioconductor.org/packages/broadSeq/ |
| Package Downloads Report | Download Stats |