Repository Index

Benchmarking analysis of data integration tools

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

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

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

• r
• rstats
• r-package

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

Probabilistic cell segmentation for in situ spatial transcriptomics

A Network Integration Approach for Drug-Target Interaction Prediction

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

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

MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.

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

PhyloNetworks: a julia package with utilities for phylogenetic networks

Open-source software for exploring and analyzing large, high-dimensional image-derived data.

• cellprofiler-analyst
• cellprofiler
• image-analysis
• machine-learning

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