A collection of Jupyter notebooks and other guides supporting data and tools available at Allen Brain Cell (ABC) Atlas Access. These resources were designed for researchers with more limited programming experience. For more extensive data access options, please visit ABC Atlas Access. To explore these data sets interactively, visit the ABC Atlas. Note: both SEA-AD notebooks include a brief introduction to Google Colab for folks unfamiliar.

Getting started guide

Download and install Anaconda and GitHub Desktop on a Windows machine to access ABC Atlas Jupyter notebooks.

View the guide

Find differentially expressed genes

Use ABC Atlas single-cell RNA-seq data to identify differentially expressed genes between two cell types using Scanpy.

Run on Colab GitHub

Plot Gene Expression in scRNA-seq data

Plot VGluT1, VGluT2, and VGluT3 expression across mouse midbrain cell types using ABC Atlas data.

Run on Colab GitHub

Plot Imputed Gene Expression in MERFISH data

Plot imputed Chrna7 and Chrm1 expression in CA1 glutamatergic neurons using ABC Atlas spatial transcriptomics data.

Run on Colab GitHub

Identify Aging-Related Genes

Identify and plot aging-related differentially expressed genes across mouse oligodendrocyte cell types using ABC Atlas data.

Run on Colab GitHub

SEA-AD Data Access

A template for browsing, downloading, and loading SEA-AD single-cell data into AnnData object.

Run on Colab GitHub

SEA-AD MTG data exploration

Download SEA-AD MTG single-nucleus RNA-seq data and assess how Sst interneurons change in AD.

Run on Colab GitHub