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debrowser

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

Interactive Differential Expresion Analysis Browser


Bioconductor version: Development (3.19)

Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. By changing the parameters, users can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With DEBrowser users can prepare plots without writing any code. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, ma plots and Heatmaps.

Author: Alper Kucukural <alper.kucukural at umassmed.edu>, Onur Yukselen <onur.yukselen at umassmed.edu>, Manuel Garber <manuel.garber at umassmed.edu>

Maintainer: Alper Kucukural <alper.kucukural at umassmed.edu>

Citation (from within R, enter citation("debrowser")):

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("debrowser")

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("debrowser")
DEBrowser Vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.31.2
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3 + file LICENSE
Depends R (>= 3.5.0)
Imports shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview, apeglm, ashr
System Requirements
URL https://github.com/UMMS-Biocore/debrowser
Bug Reports https://github.com/UMMS-Biocore/debrowser/issues/new
See More
Suggests testthat, rmarkdown, knitr
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 debrowser_1.31.2.tar.gz
Windows Binary debrowser_1.31.2.zip
macOS Binary (x86_64) debrowser_1.31.2.tgz
macOS Binary (arm64) debrowser_1.31.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/debrowser
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/debrowser
Bioc Package Browser https://code.bioconductor.org/browse/debrowser/
Package Short Url https://bioconductor.org/packages/debrowser/
Package Downloads Report Download Stats