A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
Repository Index
47,133 repositories indexed
97–120 of 191 · Most stars
Probabilistic cell segmentation for in situ spatial transcriptomics
manim cell magic for IPython/Jupyter to show the output video
- jupyter-magic
- jupyer
- manim
- ipython-magic
Images and other data from the JUMP Cell Painting Consortium
scPerturb: A resource and a python/R tool for single-cell perturbation data
- cite-seq
- database
- perturbation
- scatac-seq
Repository for Nicheformer: a foundation model for single-cell and spatial omics
Web Components engine based on VDOM, JSX, MobX & TypeScript
- webapp
- web-component
- spa
- ecmascript
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
- cellprofiler-analyst
- cellprofiler
- image-analysis
- machine-learning
Music typeset with the Lilypond system
🏃 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
F# Cold Tasks and Cancellable Tasks
- fsharp
- dotnet
- async-await
- dotnet-core
A few miscellaneous Go microbenchmarks.
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
A curated list of excellent books to learn PostgreSQL — from beginner‑friendly introductions to advanced internals, administration, and performance tuning.
- pgadmin
- postgres-extension
- postgres-tools
- postgresql
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
Inner ear models for Python
- python
- cochlea
- inner-ear
- model
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
A lightweight cron scheduler for the async job worker Que
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
Emacs mode for LESS CSS (lesscss.org), with support for compile-on-save
A curated list of awesome cytodata resources https://www.cytodata.org/awesome-cytodata/
- awesome-list
- awesome
- image-analysis
- morphology
Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
- biology
- fluorescence
- image-analysis
- image-processing