Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
- cancer-genomics
- cnv-detection
- single-cell
- phylogeny
Repository Index
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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
Open source tumor evidence matching for sequencing labs and hospitals without molecular tumor boards. Research prototype; oncologist review required.
- bioinformatics
- cancer-research
- computational-biology
- drug-repurposing
Repository for Nicheformer: a foundation model for single-cell and spatial omics
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.
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
LLM for Drug Editing, ICLR 2024
- chatgpt
- conversation
- drug
- drug-discovery
Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
- disentanglement
- drug-discovery
- genomics
- perturbation
TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524
- self-attention
- compound-protein-interaction
- transformercpi
- structure-free-virtual-sreening
Accurate and efficient spot detection for microscopy data
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
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
code to run sei and obtain sei and sequence class predictions
Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
Structural variant detection and association testing
PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.
The repository host gives no description.
Toolbox for the analysis of smFISH images.
- pattern-classification
- rna-localization
- segmentation
- smfish
BulkFormer: A large-scale foundation model for human bulk transcriptomes
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
- computational-biology
- bioinformatics
- graph-convolution
- deep-learning
PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).
- deep-generative-model
- deep-learning
- single-cell-data-integration
- single-cell-multiomics