Repository Index

Fast, sensitive and accurate integration of single-cell data with Harmony

• scrna-seq
• algorithm
• data-integration
• r

Spatial Single Cell Analysis in Python

• single-cell-rna-seq
• single-cell-genomics
• spatial-transcriptomics
• spatial-analysis

Generative biopolymer design with rich conditioning.

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

• dataset
• dna
• dna-processing
• dna-training

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq

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

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

Official repository for the ProteinGym benchmarks

• benchmark
• computational-biology
• protein
• protein-design

Sequential regulatory activity predictions with deep convolutional neural networks.

Benchmarking analysis of data integration tools

The repository host gives no description.

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

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

Schema and generated objects for biolink data model and upper ontology

• biolink
• monarchinitiative
• gene-ontology
• datamodel

RNA-seq prediction with deep convolutional neural networks.

Bi-Directional Equivariant Long-Range DNA Sequence Modeling

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

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

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

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