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debrowser

Interactive Differential Expresion Analysis Browser

Bioconductor version: 3.24 · Package version: 1.41.2

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.

Installation

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

BiocManager::install("debrowser")

Details

MaintainerAlper Kucukural <alper.kucukural@umassmed.edu>
AuthorAlper Kucukural [aut, cre], Onur Yukselen [aut], Manuel Garber [aut]
LicenseGPL-3 + file LICENSE
URLhttps://github.com/UMMS-Biocore/debrowser, https://debrowser.readthedocs.io
Bug Reportshttps://github.com/UMMS-Biocore/debrowser/issues/new
Downloads rank600
Source branchdevel
biocViewsChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packagedebrowser_1.41.2.tar.gz
Windows binary (x86_64)debrowser_1.41.2.zip
macOS binary (arm64)debrowser_1.41.2.tgz
macOS binary (x86_64)debrowser_1.41.2.tgz
Dependencies

Depends: R (>= 4.2.0)

Imports: shiny, jsonlite, shinyjs, shinyBS, shinyWidgets, gplots, DT, ggplot2, annotate, AnnotationDbi, DESeq2, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, org.Hs.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, colourpicker, plotly, heatmaply, bslib (>= 0.7.0), htmltools

Suggests: testthat (>= 3.2.0), rmarkdown, RSQLite, knitr, digest, shinymanager (>= 1.0.4), shinytest2, chromote, DBI, Harman, pathview, org.Mm.eg.db, apeglm, ashr, commonmark, enrichplot, fgsea, ipaddress (>= 1.0), mockery, msigdbr, openssl, scrypt, UpSetR, DOSE, ellmer (>= 0.1.0), keyring, whisker, withr, xml2