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DCQ: An algorithm to infer changes in quantities of immune cell sub-populations

Using DCQ on the website

A version of DCQ application is freely available and operational on different browsers including FireFox version 22 (22.0 and higher),
Chrome version 28 (28.0.1500.72 and higher), Safari version 6 (6.0.2 and higher) and Explorer version 10 (10.0.9200 and higher).

Users interested in commercial applications should contact Irit Gat-Viks.

DCQ application manual

The DCQ application manual is available here. The manual provides instructions on how to apply the entire DCQ analysis automatically.

Example files

DCQ application takes the following inputs:

1. An immune cell compendium, consisting of transcriptional profiles of isolated immune cell subsets, taken from various tissues, stimulations and time points;

2. A collection of immune cell surface markers designed to discriminate between the immune cell types included in the compendium

3. RNA-seq or microarray differential gene expression profiles of a test sample compared to a reference sample.

Here, inputs (1) and (2) are provided as part of the application.

input (3), the differential gene expression file, should be uploaded as a data file by the user (an example file).
Additional explanations about the input file format and pre-processing are in the manual file.

The people behind DCQ

DCQ application was developed in a joint work of:
- Dr. Irit Gat-Viks's System Genetics and Immuno-Genomics Laboratory at the Cell Research and Immunology Department,
Faculty of Life Sciences, Tel Aviv University, Israel;
- Dr. Ido Amit's Immuno-Genomics Laboratoty at the Immunology Department,
Weizmann Institute of Science, Rehovot, Israel.
- Dr. Michal Mandelboim at the Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel

References

[1] Zeev Altboum, Yael Steuerman, Eyal David, Zohar Barnett Itzhaki, Liran Valadarsky, Hadas Keren-Shaul, Tal Meningher, Ella Mendelson, Michal Mandelboim,
Irit Gat-Viks and Ido Amit. Digital cell quantification identifies global immune cell dynamics during Influenza infection. Molecular Systems Biology 2014, 10(2):720

Feedback

For any questions, bugs and suggestions please contact: Yael Steuerman.

Copyright information

Copyrights Tel-Aviv University, Israel (2013).

The name of contributors may be used to endorse or promote products derived from this software without specific prior written permission.

This software is provided "AS IS," without a warranty of any kind. ALL EXPRESS OR IMPLIED CONDITIONS,
REPRESENTATIONS AND WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT, ARE HEREBY EXCLUDED.

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