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In this video I demonstrate how to use iDEP (integrated Differential Expression and Pahtway analysis) to analyze an RNA-Seq data concerning ...
YouTube-Steven Ge
IDEP design framework
Example data and documentation
Customizing your method
Single gene analysis
Downloading high-resolution maps
Selecting top 2,000 genes
Interpreting principal components
StringDB API
Interactive Network
Co-expression networks
RNAseq #transcriptome #iDEP In this video, I have tried to solve the questions related to the webtool tool (iDEP) that can be used for ...
YouTube-Dr. Asif's Mol. Biology
Intro
Upload read count data
New features in iDEP
Saving high resolution figure
Exporting data
Heat map
K-means analysis
Mutant vs wild type analysis
Pathway tab
Biocluster analysis
iDEP (http://ge-lab.org/idep/) is a software for interactively analyze RNA-seq data. When coupled with vast uniformally proccessed RNA-seq ...
Download RNA-seq data
Create experiment design file
Adjust quality criteria
This is a demo for using iDEP (http://ge-lab.org/idep/) to analyze RNA-seq data. This follows chapter 22 of the RNA Bioinformatics, ...
Gene-level data
IDEP preprocessing
Customizing the color scheme
Finding the optimal number of clusters
PCA loadings
Setting reference levels
Downloading gene list
Heat shock response in the mutant
Hsf1-dependent and independent pathways
rnaseq #publicdatabase #transcriptome #idep In this video, how we can analyze public RNA-seq datasets using iDEP tool.
Analyze Public Rns Data Set for Nine Species
Search Your Keywords
Download the Experimental Design File
Pre-Processing
I show some screen shots of iDEP, a web-based bioinformatics tool for exploratory data analysis, differential gene expression, ...
Intro to iDEP
Finding differentially expressed genes
Identify overrepresented transcription factor binding motifs
Pathway analysis
How to run iDEP (http://bioinformatics.sdstate.edu/idep) locally. This is for Windows 10. Updated steps are listed on the GitHub page ...
Introduction
Install Docker Desktop
Install WSL2 from PowerShell
Start Docker Desktop
Start the iDEP Docker container
Start iDEP from a web browser
Install as an R package
Install in developer mode
https://togotv.dbcls.jp/20200118.html iDEP (integrated Differential Expression and Pathway analysis)は、ウェブブラウザ上でRNA-seqデータ解析 ...
YouTube-TogoTV
RNA #rnaseq #analysis #transcriptomedata #IDEP In this video, I have given a demo of webtool tool (IDEP) that can be used for complete RNA ...
Creating a CSV file
Upload data
RNA-seq heatmap
Interactive heat map
Principal component analysis
PCA analysis
Differential expression of genes
Differential expression of genes Level 2
Network diagram
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YouTube-i-dep official
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i-dep web http://i-dep.tokyo/ YouTube https://youtube.com/@idepofficial twitter https://twitter.com/idep_official/ instagram ...
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Instagram
i-dep web http://i-dep.tokyo/ YouTube https://youtube.com/@idepofficial twitter ...
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