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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.7.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 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
| 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_1.7.0.tar.gz |
| Windows Binary (x86_64) | broadSeq_1.7.0.zip |
| macOS Binary (big-sur-x86_64) | broadSeq_1.7.0.tgz |
| macOS Binary (sonoma-arm64) | broadSeq_1.7.0.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 |