SSAM (Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation)

📊 Identify cell types and pathways affected by genetic risk loci.

Ultrafast GPU-enabled QTL mapper

A thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"

WES HLA Typing based on multiple alternative tools

Interpretation of cell states using reference single-cell maps

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

Notebooks for 6.S088 IAP 2023

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

Single cell omics biology annotations

detecting spatial patterns of allele-specific expression

Explanation to key concepts in ML

Precision Medicine Knowledge Graph (PrimeKG)

Integrated pipeline for multiplexed image analysis

SNV calling from single cell sequencing

Course website for Johns Hopkins BSPH Statistical Computing (Biostatistics 140.776)

scover

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

Hypergraph Factorisation

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

Code for single-cell eQTL analysis of memory T cell data in Nathan, et al. bioRxiv (2021)

Gene group activity utility functions for Scanpy

Multi-resolution Variational Inference

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data