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Deep universal probabilistic programming with Python and PyTorch

Python 8,654 984 Updated Feb 5, 2025

scTM: A package for topic modelling in transcriptomics data

Python 10 Updated May 1, 2024

CAST package

Python 29 3 Updated Oct 26, 2024

RNA Velocity generalized through dynamical modeling

Python 425 105 Updated Dec 9, 2024

Zanglab k8 Services

1 Updated May 9, 2024

Code and Simulations using Bayesian Approximate Kernel Regression (BAKR)

C++ 11 3 Updated Jan 31, 2019

This is a curated list of sources related to Gaussian Process, including papers, discussions, implementations and applications.

2 Updated Apr 15, 2024

Python notebooks for Optimal Transport between Gaussian Mixture Models

Jupyter Notebook 41 9 Updated Apr 24, 2021

Spatiotemporal modeling of spatial transcriptomics

Python 260 32 Updated Dec 25, 2024

R package for CS-CORE, a statistical method for cell-type-specific co-expression inference from single cell RNA-sequencing data

R 18 Updated Oct 1, 2023

A Python/R package for fitting linear mixed models for genome-wide association studies among related individuals

HTML 7 Updated Nov 11, 2024

Dependency-aware deep generative models for multitasking analysis of spatial genomics data

Jupyter Notebook 33 2 Updated Jul 10, 2024

Probabilistic Alignment of Spatial Transcriptomics Experiments

Python 84 18 Updated May 26, 2023

Bayesian optimization in PyTorch

Jupyter Notebook 3,170 415 Updated Feb 11, 2025

Methods and Implements of Deep Clustering

2,910 419 Updated Aug 25, 2024

CNN based segmentation codes

Python 47 17 Updated Jan 19, 2023

MONAI Tutorials

Jupyter Notebook 1,972 700 Updated Feb 11, 2025

Short Course on Multi-Omics

HTML 13 11 Updated Apr 21, 2023

CeLEry: cell location recovery in single-cell RNA sequencing

Jupyter Notebook 33 3 Updated Jan 24, 2025

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

HTML 157 23 Updated Jan 26, 2024

A collection of tools for Hi-C data analysis

567 126 Updated Jan 25, 2025

scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics

R 88 26 Updated Feb 5, 2025

Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics (STAGATE software based on pyG framework)

Python 53 7 Updated Nov 10, 2023

Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics

Python 68 11 Updated Mar 5, 2022
Jupyter Notebook 28 9 Updated Dec 15, 2021

repository for Universal Domain Adaptation through Self-supervision

Python 121 19 Updated Dec 9, 2020

GDA-AM solves a wide range of minimax problems

Jupyter Notebook 7 1 Updated Jun 2, 2022

Image-to-Image Translation in PyTorch

Python 23,519 6,373 Updated May 14, 2024

software to detect doublets

Python 88 13 Updated Dec 28, 2024

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

3,299 1,004 Updated Dec 4, 2024
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