Protocols

DEBrowser specifications

Information


Unique identifier OMICS_20500
Name DEBrowser
Interface Application programming interface
Restrictions to use None
Input data A count data obtained from RNA-Seq or another high-throughput sequencing experiment in the form of matrix values.
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Manuel Garber
  • person_outline Alper Kucukural

Additional information


https://github.com/UMMS-Biocore/debrowser

Information


Unique identifier OMICS_20500
Name DEBrowser
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.8.4
Stability Stable
Requirements
AnnotationDbi, limma, methods, stats, RColorBrewer, gplots, graphics, IRanges, GenomicRanges, utils, testthat, S4Vectors, grDevices, SummarizedExperiment, edgeR, ggplot2, DESeq2, rmarkdown, knitr, reshape2, org.Hs.eg.db, annotate, org.Mm.eg.db, RCurl, R.rsp, igraph, baySeq, shiny, sva, clusterProfiler, stringi, enrichplot, colourpicker, jsonlite, heatmaply, d3heatmap, DOSE, R(>=3.5.0), pathview, shinydashboard, plotly, DT, shinyBS, shinyjs, V8, googleAuthR, Harman
Maintained Yes

Download


download.png

Versioning


No version available

Documentation


Maintainers


  • person_outline Manuel Garber
  • person_outline Alper Kucukural

Additional information


https://github.com/UMMS-Biocore/debrowser

Publication for DEBrowser

DEBrowser citation

call_split

Gene expression profiling in a mouse model of retinal vein occlusion induced by laser treatment reveals a predominant inflammatory and tissue damage response

2018
PLoS One
PMCID: 5846732
PMID: 29529099
DOI: 10.1371/journal.pone.0191338
call_split See protocol

[…] including normalisation between samples, empirical Bayes shrinkage for dispersion estimation and for fold-change estimation, and correction for multiple testing. Gene ontology analysis was done with debrowser 1.2.4.2 and GO.db 3.4.0. The data are available under the accession number GSE101398 at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101398. […]

DEBrowser institution(s)
Bioinformatics Core, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA; Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
DEBrowser funding source(s)
Supported by fund from the National Human Genome Research Institute NHGRI grant #U01 HG007910-01 and the National Center for Advancing Translational Sciences grant #UL1 TR001453-01.

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