User's Guide

Welcome to IDEAmex

IDEAMEX Integrated Differential Expression Analysis MultiEXperiment ( a WEB server to perform differential expression analyses of RNA-Seq by four different Bioconductor packages, it also integrates the information outcomes. The IDEAMEX pipeline needs a raw count table for as many desired replicates and conditions, allowing the user to select which conditions will be compared, instead of doing all-vs-all comparisons. The whole process consists of three steps 1) Data Analysis: that allows a preliminary analysis for quality control based on the data distribution per sample, using different types of graphs; 2) Differential expression: performs the differential expression analysis using the bioconductor packages: edgeR[1], limma[2], DESeq2[3] and NOISeq[4], and generates reports for each method; 3) Result integration: the integrated results are reported using Venn diagrams and text lists. Our server allows an easy and friendly visualization of results, providing an easy interaction during the analysis process, as well as error tracking and debugging by providing output log files.

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Date: 17/04/24
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RNA-Seq example file1 RNA-Seq example file2 (batch effect)

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Jiménez-Jacinto V, Sanchez-Flores A and Vega-Alvarado L (2019) Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis. Front. Genet. Vol 11, pg 279.