GigaTIME: Multimodal AI generates virtual population for tumor microenvironment modeling (Cell)

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

Interactive spatial omics for thousands of images across many assays and formats | https://rakaia.io/

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)

A Python package for unsupervised analysis of spatial (prote)omics data.

A unifying bioinformatics framework for organelle proteomics

Nextflow version of Sopa - spatial omics pipeline and analysis

Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry

GRaph-based Analysis of Subcellular/Spatial Proteomics

A curated collection of papers, codes, and resources for cross-modal translation/prediction/generation between histopathological imaging and omics (genomics, proteomics, etc.), including histopathology-to-mIF image generation, histopathology-to-genomic prediction, etc.

Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry

Spatial query for spatial omics data

Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry

Custom software written for analysis of spatial proteomics data from fetal lung acquired in the HDCA project.

Distinct mesenchymal cell states mediate prostate cancer progression

Assessing sub-cellular resolution in spatial proteomics experiments

Analysis code for the paper "Using Adjusted Local Assortativity with Molecular Pixelation unveils colocalization of membrane proteins with immunological significance"

Spatial Omics Living review

Multi-modal integration of single-cell and spatial proteomics data

Traitement statistique de données omiques