MUSE is a deep learning approach characterizing tissue composition through combined analysis of morphologies and transcriptional states for spatially resolved transcriptomics data.
☆38May 10, 2022Updated 4 years ago
Alternatives and similar repositories for MUSE
Users that are interested in MUSE are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Identify spatial domain☆92May 29, 2025Updated last year
- Learning notes for DBiT-Notes☆11Nov 28, 2024Updated last year
- ☆23Mar 29, 2023Updated 3 years ago
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆49Aug 7, 2021Updated 4 years ago
- A novel machine learning pipeline to analyse spatial transcriptomics data☆253Jul 12, 2026Updated last week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- qtools has helper functions to submit jobs to compute clusters (PBS on TSCC, SGE on oolite) from within Python☆21Sep 20, 2023Updated 2 years ago
- Her2 Breast Cancer Project☆104Nov 27, 2022Updated 3 years ago
- An unsupervised scRNA-seq analysis workflow with graph attention networks☆25May 14, 2023Updated 3 years ago
- [NeurIPS 2025] Implementation for the paper "Modeling Microenvironment Trajectories on Spatial Transcriptomics with NicheFlow"☆25Nov 4, 2025Updated 8 months ago
- AESTETIK: Convolutional autoencoder for learning spot representations from spatial transcriptomics and morphology data☆25Updated this week
- ClusterMap for multi-scale clustering analysis of spatial gene expression☆46Jun 13, 2025Updated last year
- Re-analysis of data provided by Gihawi et al. 2023 bioRxiv☆27Aug 8, 2023Updated 2 years ago
- ☆31Aug 2, 2023Updated 2 years ago
- ☆162Mar 19, 2024Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A Deep Learning-Based Model for the integration, cross-dataset cross-modality generation, self augmentation and matched multi-omics simul…☆17Aug 9, 2025Updated 11 months ago
- ☆12Nov 20, 2023Updated 2 years ago
- A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.☆38Jul 7, 2026Updated 2 weeks ago
- SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph con…☆265Feb 9, 2026Updated 5 months ago
- ☆29Apr 26, 2024Updated 2 years ago
- FA2021 Bootcamp course website for the incoming cohort of the Bioinformatics & Systems Biology Ph.D. program☆20Sep 16, 2021Updated 4 years ago
- ☆11Sep 7, 2023Updated 2 years ago
- CSCS User Lab Day – Meet the Swiss National Supercomputing Centre☆13Sep 12, 2025Updated 10 months ago
- PAST: a Prior-based self-Attention method for Spatial Transcriptomics☆13Mar 1, 2025Updated last year
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- ☆13Feb 15, 2024Updated 2 years ago
- Pipeline for analyzing rare mutations in metagenome-assembled genomes☆10Apr 4, 2025Updated last year
- Haiku: Linking Spatial Biology and Clinical Histology via Tri-Modal Contrastive Learning☆23May 9, 2026Updated 2 months ago
- ☆34Jan 27, 2025Updated last year
- This repository contains the scripts developed for the analysis of CRC samples processed with the 10x VISIUM Spatial Transcriptomics tech…☆12Feb 7, 2023Updated 3 years ago
- ☆18Jul 30, 2022Updated 3 years ago
- xGAP is an efficient, modular, extensible and fault-tolerant pipeline for massively parallelized genomic analysis/variant discovery from …☆11Oct 21, 2020Updated 5 years ago
- Reproducibility code for the manuscript: 'Inferring and perturbing cell fate regulomes in human cerebral organoids☆31Aug 8, 2023Updated 2 years ago
- Code of the paper "DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images"☆13May 12, 2026Updated 2 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- ViReport analysis of COVID-19 using GISAID data☆20Sep 20, 2020Updated 5 years ago
- ☆23Feb 19, 2020Updated 6 years ago
- ☆13Mar 29, 2024Updated 2 years ago
- This repository includes codes and data example used in the "Integrative Spatial Analysis Reveals Tumor Heterogeneity and Immune Colon…☆16May 26, 2025Updated last year
- ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method …☆101Feb 11, 2026Updated 5 months ago
- Python Implementation of the CoLlAGe radiomics descriptor. CoLlAGe captures subtle anisotropic differences in disease pathologies by meas…☆20Aug 14, 2023Updated 2 years ago
- ☆71Jan 18, 2023Updated 3 years ago