UCE is a zero-shot foundation model for single-cell gene expression data
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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
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
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
PhyloNetworks: a julia package with utilities for phylogenetic networks
OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.
Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
- disentanglement
- drug-discovery
- genomics
- perturbation
Interpretable bilinear attention network with domain adaptation improves drug-target prediction.
Data visualisation web components for the life sciences.
- biohackeu21
- bioinformatics
- visualization
- webcomponents
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
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
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
- r
- neuroanatomy-toolbox
- cran
- neuron
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
- epigenomics
- pattern-search
- data-visualization
- interactive-machine-learning
High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
- single-cell
- scrna-seq
- scatac-seq
- deep-neural-networks
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
Predicting Cell Health with Morphological Profiles
- carpenter-lab
- morphological-profiling
- crispr
- cell-painting