Repository Index

The repository host gives no description.

Code for the ProteinMPNN paper

The repository host gives no description.

• foundation-model
• gpt
• single-cell

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

• drug-repurposing
• deep-learning
• drug-target-interactions
• toolkit

Foundation Models for Genomics & Transcriptomics

• genomics
• deep-learning
• transformer
• dna

Precision Medicine Knowledge Graph (PrimeKG)

• knowledge-graph
• precision-medicine
• therapeutics
• bioinformatics

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

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

• sequence-alignment
• edit-distance
• levehnstein-distance
• library

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

The repository host gives no description.

Reference mapping for single-cell genomics

• single-cell
• deep-learning
• rna-seq-analysis
• data-integration

Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

• dna
• language-model
• variant-effect-prediction
• genomics

The repository host gives no description.

Schema and generated objects for biolink data model and upper ontology

• biolink
• monarchinitiative
• gene-ontology
• datamodel

Bi-Directional Equivariant Long-Range DNA Sequence Modeling

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

• histology
• wsi-images
• pan-cancer-analysis
• genomics

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

scPerturb: A resource and a python/R tool for single-cell perturbation data

• cite-seq
• database
• perturbation
• scatac-seq

Repository for Nicheformer: a foundation model for single-cell and spatial omics

The repository host gives no description.

🏃 The go-to single-cell Foundation Model

• batch-correction
• cell-biology
• celltype-annotation
• denoising

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

• disentanglement
• drug-discovery
• genomics
• perturbation