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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talk with NCBI entrez using R
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
Probabilistic cell segmentation for in situ spatial transcriptomics
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
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.
🏃 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
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
Interpretable bilinear attention network with domain adaptation improves drug-target prediction.
Data visualisation web components for the life sciences.
- biohackeu21
- bioinformatics
- visualization
- webcomponents
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
The repository host gives no description.
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
GeneCompass
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
code to run sei and obtain sei and sequence class predictions
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
Rails frontend to The Genome Institute's drug gene interaction database.
PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.