debrowser

DOI: 10.18129/B9.bioc.debrowser    

debrowser: Interactive Differential Expresion Analysis Browser

Bioconductor version: Release (3.6)

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>, Manuel Garber <manuel.garber at umassmed.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("debrowser")

Documentation

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

Details

biocViews	ChIPSeq, Clustering, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version	1.6.8
In Bioconductor since	BioC 3.3 (R-3.3) (2 years)
License	GPL-3 + file LICENSE
Depends	R (>= 3.3.0), shiny, ggvis, jsonlite, shinyjs
Imports	DT, ggplot2, RColorBrewer, annotate, gplots, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, baySeq, d3heatmap, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, V8, methods, sva, shinydashboard, RCurl, pathview, shinyBS, googleAuthR
LinkingTo
Suggests	testthat, rmarkdown, knitr, R.rsp
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
Build Report

Package Archives

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

Source Package	debrowser_1.6.8.tar.gz
Windows Binary	debrowser_1.6.8.zip
Mac OS X 10.11 (El Capitan)	debrowser_1.6.8.tgz
Source Repository	git clone https://git.bioconductor.org/packages/debrowser
Package Short Url	http://bioconductor.org/packages/debrowser/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive