debrowser

DOI: 10.18129/B9.bioc.debrowser    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see debrowser.

Interactive Differential Expresion Analysis Browser

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	DEBrowser Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.24.1
In Bioconductor since	BioC 3.3 (R-3.3) (6.5 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
LinkingTo
Suggests	testthat, rmarkdown, knitr
SystemRequirements
Enhances
URL	https://github.com/UMMS-Biocore/debrowser
BugReports	https://github.com/UMMS-Biocore/debrowser/issues/new
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	debrowser_1.24.1.tar.gz
Windows Binary	debrowser_1.24.1.zip
macOS Binary (x86_64)	debrowser_1.24.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/debrowser
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/debrowser
Package Short Url	https://bioconductor.org/packages/debrowser/
Package Downloads Report	Download Stats