broadSeq
This is the development version of broadSeq; to use it, please install the devel version of Bioconductor.
broadSeq : for streamlined exploration of RNA-seq data
Bioconductor version: Development (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")
# 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")
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 | 0.99.3 |
In Bioconductor since | BioC 3.20 (R-4.4) |
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_0.99.3.tar.gz |
Windows Binary (x86_64) | broadSeq_0.99.3.zip (64-bit only) |
macOS Binary (x86_64) | broadSeq_0.99.3.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 |