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Bioconductor - debrowser (development version)

debrowser

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

Interactive Differential Expresion Analysis Browser

Bioconductor version: Development (3.22)

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 "4.5") 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")
Details biocViews ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software Version 1.37.0 In Bioconductor since BioC 3.3 (R-3.3) (9 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 Package Archives

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

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