Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
- cancer-genomics
- cnv-detection
- single-cell
- phylogeny
Repository Index
47,133 repositories indexed
49–72 of 88 · Most stars
Mir (backports): Sparse tensors, Hoffman
- mir
- glas
- blas
- mir-glas
The RAW JavaScript Quaternion library
- quaternion
- angle
- conjugate
- math
scPerturb: A resource and a python/R tool for single-cell perturbation data
- cite-seq
- database
- perturbation
- scatac-seq
A Python interface to access neuroanatomical atlases
- neuroscience
- python
- microscopy
- registration
Repository for Nicheformer: a foundation model for single-cell and spatial omics
🏃 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
Automated 3D brain registration with support for multiple species and atlases.
- registration
- atlases
- brain
- neuroscience
⚡ Open-source software for deep learning-based digital pathology
- deep-learning
- machine-learning
- digital-pathology
- computational-pathology
A strongly-typed genetic programming framework for Python
- python
- ipynb
- genetic-programming
- framework
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
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.
Data Access Client for Global Surface Summary of the Day (GSOD) Weather Written in R
- r
- weather-data
- gsod
- ncdc
PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.
A platform independent tensor library with autograd for the JVM
- java
- library
- deep-neural-networks
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
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.
Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
A matrix package for common lisp building on work by Mark Hoemmen, Evan Monroig, Tamas Papp and Rif.
Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
- foundation-models
- gpt
- single-cell
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics