debrowser

DOI: 10.18129/B9.bioc.debrowser    

Interactive Differential Expresion Analysis Browser

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("debrowser", version = "3.8")

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 1.10.4
In Bioconductor since BioC 3.3 (R-3.3) (2.5 years)
License GPL-3 + file LICENSE
Depends R (>= 3.5.0)
Imports shiny, jsonlite, shinyjs, shinydashboard, shinyBS, pathview, gplots, DT, ggplot2, RColorBrewer, annotate, 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, RCurl, googleAuthR, enrichplot, colourpicker, plotly, heatmaply, Harman
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
Links To Me
Build Report  

Package Archives

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

Source Package debrowser_1.10.4.tar.gz
Windows Binary debrowser_1.10.4.zip
Mac OS X 10.11 (El Capitan) debrowser_1.10.4.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 http://bioconductor.org/packages/debrowser/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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