Repository Index

AlphaFold 3 inference pipeline.

Biological foundation modeling from molecular to genome scale

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

• variant-calling
• genomics
• vcf-manipulation
• genotyping

RNA Velocity generalized through dynamical modeling

Graph-linked unified embedding for single-cell multi-omics data integration

• bioinformatics
• deep-learning
• single-cell
• single-cell-multiomics

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

• bioinformatics
• taxonomy
• cross-platform
• lineage

Schema and generated objects for biolink data model and upper ontology

• biolink
• monarchinitiative
• gene-ontology
• datamodel

Bi-Directional Equivariant Long-Range DNA Sequence Modeling

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

• cancer-genomics
• cnv-detection
• single-cell
• phylogeny

OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.

Interpretable bilinear attention network with domain adaptation improves drug-target prediction.

Python package for image-based profiling

• cytominer
• microscopy
• morphological-profiling
• python

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

• protein
• protein-sequences
• protein-design
• representation-learning

The repository host gives no description.

Integrated pipeline for multiplexed image analysis

• multiplexed-imaging
• python

Methods for Image-Based Cell Profiling

• profiling
• microscopy
• r

Predicting Cell Health with Morphological Profiles

• carpenter-lab
• morphological-profiling
• crispr
• cell-painting

Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.

• postgres
• postgresql
• python
• infectious-disease

A flexible Julia toolkit for high-dimensional cellular profiles

• julia
• morphological-analysis
• high-content-screening

DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods. The software structure is such that data can be processed either at the command line or using a graphical user-interface. Detecdiv classification models include : image classification and regression, semantic segmentation, LSTM networks to analyze data and image timeseries.

Interpretable modeling of cellular responses to drug perturbations using cycle consistence learning

Interpretable drug response prediction with graph neural networks over drugs, cell lines, and genes.