The current DNA sequencing technologies and their high-throughput yield, allowed 
the thrive of genomic and transcriptomic experiments but it also have generated 
big data problem. Due to this exponential growth of sequencing data, also the 
complexity of managing, processing and interpreting it in order to generate 
results, has raised. Therefore, the demand of easy-to-use friendly software and 
websites to run bioinformatic tools is imminent. In particular, RNA-Seq and 
differential expression analysis have become a popular and useful method to 
evaluate the genetic expression change in any organism. However, many scientists 
struggle with the data analysis since most of the available tools are 
implemented in a UNIX-based environment. Therefore, we have developed the web 
server IDEAMEX (Integrative Differential Expression Analysis for Multiple 
EXperiments). 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 main 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 with or without batch effect error awareness, using the bioconductor 
packages, NOISeq, limma-Voom, DESeq2 and edgeR, and generate reports for each 
method; (3) Result integration: the obtained results the integrated results are 
reported using different graphical outputs such as correlograms, heatmaps, Venn 
diagrams and text lists. Our server allows an easy and friendly visualization 
for results, providing an easy interaction during the analysis process, as well 
as error tracking and debugging by providing output log files. The server is 
currently available and can be accessed at http://www.uusmb.unam.mx/ideamex/ 
where the documentation and example input files are provided. We consider that 
this web server can help other researchers with no previous bioinformatic 
knowledge, to perform their analyses in a simple manner.