debrowser
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see debrowser.
Interactive Differential Expresion Analysis Browser
Bioconductor version: 3.9
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("debrowser")):
Installation
To install this package, start R (version "3.6") 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")| DEBrowser Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ChIPSeq, Clustering, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software |
| Version | 1.12.3 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 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, d3heatmap, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview |
| System Requirements | |
| URL | https://github.com/UMMS-Biocore/debrowser |
| Bug Reports | https://github.com/UMMS-Biocore/debrowser/issues/new |
See More
| Suggests | testthat, rmarkdown, knitr, R.rsp |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | debrowser_1.12.3.tar.gz |
| Windows Binary | debrowser_1.12.3.zip |
| Mac OS X 10.11 (El Capitan) | debrowser_1.12.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/debrowser |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/debrowser |
| Bioc Package Browser | https://code.bioconductor.org/browse/debrowser/ |
| Package Short Url | https://bioconductor.org/packages/debrowser/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |