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)

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.

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.