bohdan-khomtchouk / microscope

ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps

MicroScope

About

We propose a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data, including integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network visualization.

MicroScope is financially supported by the United States Department of Defense (DoD) through the National Defense Science and Engineering Graduate Fellowship (NDSEG) Program. This research was conducted with Government support under and awarded by DoD, Army Research Office (ARO), National Defense Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a.

Please cite: "Khomtchouk BB, Hennessy JR, Wahlestedt C. “MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps.” BMC Bioinformatics. 2016, 17:390. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1260-x" within any source that makes use of any methods inspired by MicroScope.

Usage (for general public)

http://microscopebioinformatics.org/

Installation (for developers only)

Requirements for developers

• R programming language
  • RStudio

How to run (for developers only)

Git clone this repo to your computer, and in RStudio type:

• setwd("~/path/to/my_directory/Microscope")
• install.packages("shiny")
• library(shiny)
• library(shinyapps)
• install.packages("d3heatmap")
• library(d3heatmap)
• install.packages("RColorBrewer")
• library(RColorBrewer)
• install.packages("htmlwidgets")
• library(htmlwidgets)
• install.packages("networkD3")
• library(networkD3)
• install.packages("data.table")
• library(data.table)
• install.packages("dplyr")
• library(dplyr)
• source("https://bioconductor.org/biocLite.R")
• biocLite("edgeR")
• library(edgeR)
• biocLite("GO.db")
• library(GO.db)
• biocLite("goseq")
• library(goseq)
• biocLite("org.Bt.eg.db")
• biocLite("org.Ce.eg.db")
• biocLite("org.Cf.eg.db")
• biocLite("org.Dm.eg.db")
• biocLite("org.Dr.eg.db")
• biocLite("org.Hs.eg.db")
• biocLite("org.Mm.eg.db")
• biocLite("org.Pt.eg.db")
• biocLite("org.Rn.eg.db")
• biocLite("org.Ss.eg.db")
• biocLite("org.Sc.sgd.db")
• runApp("microscope")

Screenshots

microscope's Issues

New UI

MicroScope logo

new set of figures

Updated screenshot

New image screenshot

pics

fig 1.1

screenshot2

Pics

New logo

screenshot3

Updated figures

DESeq2 support

Hi

First off all... Great software...
Are you thinking on adding support for DESeq2 for the DE analysis?

Thanks

Updated screenshots #2

Not working with my file

Thanks for this nice piece of software. I tried with the attached file, but I didn't get any heatmap in the heatmap tab and an error in the stats tab. Let me know what is wrong with my file.
Although the Excel screenshot is informative, you should provide a short and clear example file. But that's only my humble opinion.
samples.csv.zip

Screenshots

pics

screenshot