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Computational Tools

Data Analysis Tools

This category includes coding packages, custom gene-specific or region-specific analyses, data mapping software, and other tools for exploring underlying data from Allen Brain Map resources in new ways.

Click here to see the full database of data analysis tools.

Visualization Tools

These tools provide novel methods to visualize Allen Brain Map data such as generating reproducible plots, custom heatmaps, and imaging of brain architecture.

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Data Preprocessing, Registration, and Integration Tools

These tools either improve Allen Brain Map data or use Allen Brain Map resources to improve data generated in other groups. Data preprocessing software makes data more usable by improving the quality of the data and reformatting it for downstream analysis. Data registration software tools take an imaged brain section or other unprocessed data set and morph it to better match a reference. Similarly, data integration tools combine data from Allen Brain Map and other public sources across projects, data modalities, and brain regions into the same framework. 

Click here to see the full database of data preprocessing, data registration, and data integration tools.

Data Annotation and Segmentation Tools

These tools allow users to provide additional biological context to a dataset through annotation of gene expression data and segmentation of brain images by brain region.

Click here to see the full database of data annotation and data segmentation tools.