Computational Analysis Toolbox
This list captures a selection of public computational analysis tools available from Allen Institute scientists. Access the complete set of computational tools and resources general Allen Institute GitHub repository. Questions about these tools can be submitted in the Allen Brain Map Community Forum
The Allen Institute on GitHub
The Allen Institute GitHub space hosts software packages that use or support access to online projects, resources, publications and data sets affiliated with the Allen Institute.
Allen Brain Cell Atlas - Data Access
Jupyter notebooks that provide tutorials and examples for downloading and analysing data from the Allen Brain Cell (ABC) Atlas, including data from whole adult and aged mouse brain, whole human brain, cross-species basal ganglia, and human studies of Alzheimer's and Parkinson's disease.
Single-cell RNA-seq analysis for transcriptomic type characterization (scrattch)
A suite of R and python libraries from the Allen Institute for Brain Science for clustering, mapping, data formatting, and visualization, along with example data for demos. The majority of Allen Institute publications involving single cell transcriptomics or patch-seq use at least one of these tools.
Cell Type Mapper
A python package for mapping single sell RNA sequencing data onto a cell type taxonomy and the primary algorithm used in MapMyCells.
Community Data Challenges
Data challenges are competitions where participants solve problems using open-source datasets, providing community members a way to directly interact with data generating labs. The Allen Institute has spearheaded multiple data challenges targeting distinct scientific challenges in brain cell typing.