Repository for Nicheformer: a foundation model for single-cell and spatial omics
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🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
Fork of https://gitlab.mpcdf.mpg.de/mtr/pocketfft to simplify external contributions
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
TUM Roborace Team Software Stack - Vehicle Simulation
Accurate and efficient spot detection for microscopy data
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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
Auto-QChem is an automated workflow for the generation and storage of DFT calculations for organic molecules.
- cheminformatics
- dft-calculations
- automation
- feature
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
code to run sei and obtain sei and sequence class predictions
Integrated pipeline for multiplexed image analysis
- multiplexed-imaging
- python
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.
Variations on Kirby & Paris' hydra battles and other entertaining math in Coq (collaborative, documented, includes exercises) [maintainer=@Casteran]
- coq
- hydra-battles
- ordinal-notations
- formal-proofs
A library for placing labels in areas.
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
MAT is library for working with multi-dimensional arrays which supports efficient interfacing to foreign and CUDA code. BLAS and CUBLAS bindings are available.
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
- cell-annotation
- multiplexed-imaging
- mpif
Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.
- minerva
- microscopy
- ome
- immunofluorescence
High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations