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https://github.com/calico/borzoi
Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.
Proper citation: Borzoi (RRID:SCR_026619) Copy
BRAIN Initiative data archive for multi-modal neurophysiological and behavioral data, supporting the Brain Behavior Quantification and Synchronization (BBQS) Program. Accessible and versatile data archive for storage, processing, and curation of multimodal neurophysiological and behavioral datasets. EMBER extends established BRAIN Initiative data infrastructure, provides new data harmonization and synchronization capabilities, and supports scalable integrations for data coordination and AI driven batch processing to enable the goals of the BBQS program.
Proper citation: Ecosystem for Multi-modal Brain-behavior Experimentation and Research (RRID:SCR_026700) Copy
https://github.com/SynapseWeb/PyReconstruct
Software successor to the Reconstruct annotation tool. PyReconstruct runs on all major operating systems, breaks through legacy RAM limitations, features intuitive and collaborative curation system, and employs flexible and dynamic approach to image registration. Used to analyze, display, and publish experimental or connectomics data. Suited for generating ground truth to implement in automated segmentation, outcomes of which can be returned to PyReconstruct for proofreading and quality control.
Proper citation: PyReconstruct (RRID:SCR_027562) Copy
https://pypi.org/project/piano-integration/
Software novel variational autoencoder framework for inferring integrated latent space representations for single cell transcriptomics data that uses a negative binomial generalized linear model for stronger batch correction, and code compilation for ten times faster training than existing tools. Enables superior analyses of multiple atlases, solving challenging integration tasks across sequencing platforms, development, and species, while simultaneously preserving desired biological signals.
Proper citation: PIANO:Probabilistic Inference Autoencoder Networks for multi-Omics (RRID:SCR_027864) Copy
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