Key Resources

    We offer a select list of brainSCOPE Resources, derived from our primary analyses, to ensure quick, easy, and fully open-source access for end users Click here to access these Key Resource files. These include sample metadata, expression quantification, scCRE regions, DE genes, gene variance, scQTL callsets, GRNs, cell-to-cell networks, and predictive model results.

Raw Data

    Raw data files for PsychEncode single-cell samples, including FASTQs for snRNA-Seq, snATAC-Seq, snMultiome, and genotype data, are hosted with protected access at the Synapse data repository and other repositories. Links and descriptions for each individual dataset are available here.

Output Files

    All output files from brainSCOPE-related analyses, including the resource files and expanded analyses, as well as computer code used in the analyses are available for download here. These datasets are fully open-source.

Interactive Visualization

    Select brainSCOPE datasets, such as snRNA-Seq, scQTLs, and gene regulatory networks, can be visualized within the PsychSCREEN Single-Cell Browser. Click here to view examples for each visualization tool within PsychSCREEN.

Source Code

    Source code for snRNA-Seq data processing, scQTL detection pipelines, and deep learning model implementation used in the integrative analysis is available at the PsychENCODE GitHub repository.