Multimodal Environment for Neuroimaging and Genomic Analysis (MENGA) is a platform for the integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA aims to provide a comprehensive environment to investigate correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas.
This is the new version (MENGA 3.1), that includes two independent adds-on to use with MENGA (MENGA_GENE_EXPRESSION and MENGA_GENOMIC_PLOT).
Briefly, the first add-on extracts mRNA data in log2 values in case one wants to analyse only transcriptome data; the second extracts mRNA data in linear scale to be used to implement the genomic plot (doi: 10.1016/j.neuroimage.2016.01.058).
Therefore, the processed ABA database has remained the same: if you already have downloaded MENGA 3.0, you just need to download the updated code (code_MENGA_31.zip) and the updated manual. If you don't have the full database, you can find it at the public repositories listed below (NITRC, figshare, or FAIR at the Department website).
There are two main files: "code_MENGA_31.zip" contains all the code files, "MANUAL_MENGA_31_20160427" contains the updated manual.
Note: the genomic database is too heavy to be shared on GitHub. Please find it at: http://fair.dei.unipd.it/require-software or http://www.nitrc.org/projects/menga/ or https://figshare.com/articles/MENGA_3_1/3203395
Image data can be found in the figshare repository (dopamine PET and SPET images, https://figshare.com/articles/Image_data/2068011; MR-based water content, https://figshare.com/articles/MR_based_absolute_myelin_water_image/2068047; serotonin and dopamine D2 PET images: https://figshare.com/articles/Serotonin_and_dopamine_D2_PET_images/2068044).
We have now published the reference paper of MENGA on PlosOne, in which all the aspects of the software and its functionalities are described in details: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148744
Current version is 3.1