shiny-nanotube's Introduction

Shiny-NanoTube

Installation

Download and install RStudio (and R)
Install the NanoTube package from Bioconductor:

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

BiocManager::install("NanoTube")

Install other required and recommended libraries.

install.packages(c("shinyBS", "shinyjs", "plotly", "DT"))
BiocManager::install("qusage")

Open 'ui.R' in Shiny-NanoTube, and click 'Run'!

A first analysis

Download example data sets from the 'data' folder.
Run the Shiny-NanoTube app (either from RStudio or the web page).
In the Setup tab, load 'GSE132946.zip' in the NanoString data field, and load 'SampleData-GSE132946.csv' in the Sample info table field. A Group Column menu will appear, and open that menu to select 'outcome'.
Click the Check Samples button to ensure that the expression data and sample metadata are merged correctly. The 'Filename' and 'name' columns should match.
(Optional) Load a gmt file in the Gene set database field.
Click Analyze Data.
View results in the QC Results, Differential Expression, and Gene Set Analysis (optional) tabs.
If you're having trouble, check the Help page, raise an Issue on GitHub, or fill out the form here.

shiny-nanotube's People

Contributors

Stargazers

Watchers

shiny-nanotube's Issues

Plexset Analysis

Is there a way to configure to allow to import Plexset RCC files straight out of the nCounter without deplexing to one sample per file?

I hope this email finds you well. I'm reaching out because I'm encountering some difficulties using NanoTube for my microRNA analysis.
I wanted to inquire if it's possible to use NanoTube with microRNA data. If so, could you provide any guidance on how to properly configure it for this type of analysis?

Loading my RCC files in zip fails

I just want to load raw Rcc files and get an export with normalized values with RUVg n a matrix.

But it fails to load them. Why ?
Any help would be more than welcome.

RCC header looks like the following.

<Header>
FileVersion,1.7
SoftwareVersion,4.0.0.3
</Header>

 runApp('Desktop/NANO/Shiny-NanoTube')

Listening on http://127.0.0.1:6389
[1] "/home/jp/Desktop/NANO/Shiny-NanoTube"

Reading in .RCC files......
Checking codeset contents......
Checked gene name consistency in .RCC files.Warning: Error in [[: subscript out of bounds
  154: <Anonymous>
  153: read_merge_rcc
  152: processNanostringData
  148: eventReactiveValueFunc [/home/jp/Desktop/NANO/Shiny-NanoTube/server.R#73]
  104: ns
   97: renderText [/home/jp/Desktop/NANO/Shiny-NanoTube/server.R#155]
   96: func
   83: renderFunc
   82: output$numSamps
    1: runApp

Recommend Projects