Official repository for the ProteinGym benchmarks
- benchmark
- computational-biology
- protein
- protein-design
Repository Index
47,133 repositories indexed
49–72 of 142 · Most stars
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
Sequential regulatory activity predictions with deep convolutional neural networks.
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
Benchmarking analysis of data integration tools
The repository host gives no description.
Multi-Omics Factor Analysis
- multi-omics
- factor-analysis
- mofa
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
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
bioruby
The repository host gives no description.
UCE is a zero-shot foundation model for single-cell gene expression data
The repository host gives no description.
Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk
- bioinformatics
- exact-optimization
- metabolomics
- paired-data
Open Frontier Biomolecular Intelligence
RNA-seq prediction with deep convolutional neural networks.
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)
Ankh: Optimized Protein Language Model
Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
- cancer-genomics
- cnv-detection
- single-cell
- phylogeny
talk with NCBI entrez using R