MacSpectrum is now available as a R package. The current version can calculate MPI and AMDI using the same input files as for our web-based version. The function to plot heatmaps of signature genes along MPI will be included in future.
The R package is available upon request following our Non-Commercial-Use-License.
Using our newly launched MacBrowser, you can check the MPI/AMDI plots and gene expressions of murine bone marrow derived macrophages that were not stimulated (“M0”), or stimulated LPS+IFNγ (“M1”) or IL4+IL13 (“M2”). You can see their MPI/AMDI distributions and expression patterns of any genes. Please refer to our JCI insight publication (PMID: 30990466) for more details of the dataset.
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.
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 up.
If download window does not pop up, try this temporary fix:
Before clicking the “Download Sig Gene” button, click the “Make Heatmap” first; this will pre-calculate the MPI-signature genes; after the Gene-MPI Heatmap is generated, then click “Download Sig Gene” to download the MPI-signature genes. (for details check our user manual)
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.
We now have an additional server hosting the MacSpectrum web-application. MacSpectrum can now be run using our main server or our back-up server. Links to the two servers are also available on the home page.
MacSpectrum is a macrophage annotation system that allows comprehensive analysis of heterogeneous subpopulation and their multifaceted activation states under various in vitro and in vivo conditions. Each subpopulation identified by this system can be analyzed for cell function, intracellular signaling networks, and condition-specific signature genes.