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Session information

Connected Users

Built using R and Shiny

Chat source code is available here

What's new in MATRiX

May 07th 2019 - Fix

In volcano plot the FC cutoff is now correctly applied. Previously the value were filtered according to log2FC.

Mar 12th 2019 - Front-end

Add data summary page, hides menu pages and redirect users after data loading.

Feb 14th 2019 - Functional results

It is now possible to sort the categorie terms based on both pvalue and Fold enrichment.

Feb 14th 2019 - Jvenn results

Duplicated genes are now highlited as orange in the output table

Feb 14th 2019 - Upload

Users can now import csv data with semicolon or comma separatos by precising the decimal

Jan 25th 2019 - Bug

Correct david$getSpecieNames (Specieshm and Speciesvenn)

Jan 25th 2019 - Data

Users can now register as a team and load their data directly from the server (only for 2019 projects and logs are provided in report)

Jan 25th 2019 - MATRiX

MATRiX is now running with Shinyproxy (Spring + Docker)

Jan 21th 2019 - Increased exploration

Add features to filter the top n based on the FDR/RAW and logFC, Generate strip chart for specific genes and barplot for Volcano plot

Jan 11th 2019 - Data

MATRiX is now compatible with Microarray, ChIP-seq and RNA-seq data

Nov 30th 2018 - MATRiX

Add tootlip for distance, its now possible to export acyclic graphs in pdf and eps, correct bugs for classification enrichment with 0 nodes by inactivating donwload button

Nov 29th 2018 - Venn Diagram/HTML

Correct bugs now venn diagram table is based on genes and not probes.

Nov 5th 2018 - Venn Diagram

Remove non annotated genes.

Oct 19th 2018 - Volcano plot

Search group of genes based on regular expression.

Oct 15th 2018 - Venn Diagram

Change the library to Jvenn.

Aug 15th 2018 - Presentation/Video

Added a video to present MATRiX and add modules to import files.

Aug 10th 2018 - Upload/Volcano

You can explore your different comparisons with a volcano plot.

Aug 6th 2018 - Venn Diagram/Enrichment

Add acyclic graph if download.

Aug 4th 2018 - Heatmap/Bubble graph

You can display or not the labels within the bubbles.

Aug 3th 2018 - Heatmap/Go(Analysis)

You can now plot a bubble graph (Highcharts) that summarizes the top categories from the resulting datatable.

Jul 28th 2018 - Home/Support

You can asks your questions directly in the Support.

Jul 25th 2018 - Tutorial/Video

Soon will be added a video to summarise the application.

Jul 20th 2018 - New page

Add a Home page regrouping informatios about the app.

Jul 16th 2018 - Venn

You can now choose your color for the venn diagram.

Jul 16th 2018 - Bug fixes

Venn diagram display erros when filtering.

Jul 5th 2018 - Venn/DAVID

Add Gene functionnal classification for selected intersection(s).

Jun 26th 2018 - Add features

It's now possible to interact with the rendering table to filter the table in the aim of plotting the top n genes. For the GO enrichment it is now possible to select the rows in order to display the gene symbol according to the entrez ids.

Jun 22th 2018 - Bug fixes

For two contrasts the venn.draw function was not ordering the contrast names in the right order.

Jun 20th 2018 - MATRiX

First public release of MATRiX. Enhancement of the gui with the use of dashboard package.

Jun 18th 2018 - GO enrichment

It is now possible to query the DWS for the Heatmap and save the result in xlsx format for the different clusters

Jun 15th 2018 - DNS

Adding DNS for the MATRiX application (

Jun 10th 2018 - Venn diagram

The venn diagram FC and display of the top n genes have been added to compare the results of 2 or more contrasts.

Jun 5th 2018 - PCA/Heatmap

Display color groups side by side in the gui.

May 29th 2018 - beta-test

The service will be made available once the beta test phase is officially completed.

How to import ?

  • First click on the browse button to load the data
  • After the pop up has appeared, you will have to select the data files.
  • It is also possible to directly drag and drop your data files in the browse button
  • You need three distinct csv files, these files are respectively named xxx_pData, xxx_WorkingSet and xxx_ResTable.
  • pData : The experimental design in a 2 column table that associates samples to their respective biological conditions
  • WorkingSet : The table of the normalised expression values (log2, cpm, ...) with genes in rows and samples in columns. The first column must contain the unique gene identifier (or transcript, probe, ...).
  • ResTable : The table containing the results of differential analysis (fold change, p-value and FDR) next to a first column with unique gene identifier and a second column with the gene symbol.
  • The final step consist to select all the data at once and then confirm the selection by clicking on the open button.
  • A green message will then appear to confirm the data loading with a summary table.


  • Unique IDs and GeneName columns must appear in the statistical data and unique IDs columns for Workingset in order to import the data (RNA-seq, DNA-chips, ChIP-Seq).
  • You can select a region by handling the left click button if the files are stacked together, if it's not the case you can select the different files by maintening the Ctrl button and clicked on the files.


  • It is highly recommanded to not modify these files (removed columns, change column names ...) in the aim of not disturbing the well functionning of the application.

Upload data

Download example data files

Files configurations:

Upload project .csv files from:

2. your team's project on the server location

Data summary


Highlight gene(s): fill comma-separated GeneNames

PCA settings


Filter the datatable

You can directly filter the table by fold change and save the output table
You can directly filter the table by fold change and save the output table, genes in orange are duplicates

Here's a tracker for your different selections:

You have chosen the following comparisons

for a total of

genes with a P-value and FC treshold respectively set to


There are

significant genes

for this intersection

if you click on the top DE genes button you will plot the top

rows the of the previous table

Venn settings

A comma-separated list of x11 or hex colors.

Select your Type of Venn

Display the stat

Police's size

Find an element in list(s)

Display switch

Functional Annotation Clustering


Here's a tracker of your different parameters:

Selection of

significant features

for the following comparison(s):

Based on the

method, with a P-value and FC treshold respectively set to


Limitation to a maximum of

top regulated features per comparison according P-value.

Clustering distance method :

. Number of Clusters selected:

Graphical color settings of the groups :

are respectively :

Download the data

Table of Features from the heatmap

Cluster numbers are indicated and are in decreasing order to be matching the same order of the heatmap image. Note that on the heatmap, the clusters numbers are ordered from the bottom to the top of the image.

Table summarizing the number of features per cluster

Note that duplicated features are removed to calcuate the number of genes by cluster
Save enrichment resluts as .xlsx