HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024 (Spotlight)

A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022).

Whole exome sequencing (WES) comparison of PDAC organoids against their corresponding tissue samples

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics

onlice reproducibility guide for paper benchmarkst

Detection of spot-based spatial transcriptomics domains correlating to single-cell profiles

Convert PDF to markdown + JSON quickly with high accuracy

repository for codes to generate figures for ALTRA manuscript

Code and example of the D-SPIN framework

Visualization Package for NetworkX

Direct estimation of mean and covariance from single cell RNA seq experiments

Perturbation Analysis in the scverse ecosystem.

A sandbox for benchmarking detection of out-of-reference cells in single-cell genomics data

Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition

EBI cancer workshop course materials

Slides and Notebooks for scverse 2024

Vitessce is a visual integration tool for exploration of spatial single-cell experiments.

improved clustering pipeline for transcriptomic data

single cell foundation model for Gene network inference and more

Significance analysis for clustering single-cell RNA-sequencing data

Integrative and Reference-Informed Spatial Domain Detection for Spatial Transcriptomics

Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology

Subpopulation detection in high-dimensional single-cell data

Non-parametric density inference for single-cell analysis.

Code used to process the data of the HBCA project

A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.