Welcome to MacSpectrum!

Run a query of your macrophage samples.

If the link above does not work, Try our back-up server.

Please refer to the User Instructions for detailed explanations.

Do not have data yet? You can try MacSpectrum using our simulated data-set example.

Release v1.0.1

MacSpectrum is a macrophage annotation system that allows comprehensive analysis of heterogeneous subpopulations and their multifaceted activation states under various in vitro and in vivo conditions, including the identification of condition-specific signature genes. Each subpopulation identified by MacSpectrum can be further analyzed for cell function and intracellular signaling networks in conjunction with other programs, such as Ingenuity Pathway Analysis by Qiagen, NIH DAVID, and others.


With MacSpectrum, you can:

    1. generate MacSpectrum Plots to visualize heterogeneity of your macrophage data-sets.

    2. Identify and visualize signature gene list in macrophage subsets identified by MacSpectrum.

For other functions, including query for gene expression pattern in the existing transcriptome profiles, will be provided in the coming versions. For specific questions, please contact us.

MacSpectrum currently only accepts Ensembl ID as gene ids. And we provide two worktables to facilitate converting from Gene Names to Ensembl IDs for human and mouse genes. Please refer to the User Instructions for details.

Release Log

  • Do not have data yet? No problem!
    Now you can play with MacSpectrum with our simulated data-set (simulated_gene_cell_table, simulated_feature_file). The simulated data-set is generated by algorithm. It contains 200 “cells” and ~4500 gene ids. It also serves as an easier-to-understand example for formatting your own data-set correctly.
  • Solving the browser time-out issue during calculation of sig genes
    If you experienced browser time-out issues (like the image below) when you try to download sig genes, do not close the browser page and stay in the page for a while; as long as it still shows “Processing…”, the calculation is going on in the back-end, and when it finishes, the download window should pop […]
  • 05/01/2019 – version 1.0.1 released
    What’s new: 1) MMI (Macrophage Maturation Index) is now named as AMDI (Activation-induced Macrophage Differentiation Index). Please refer to our JCI-insight article for details. 2) Faster calculation speed with improved algorithm.


The software provided on this website may be used freely by users from academic and non-profit organizations. Users from the commercial sector should contact us.

MacSpectrum does not store user-uploaded data.

Zhou Lab @2018