Spatial omics in the browser for thousands of images across many assays and formats | https://rakaia.io/

Quantification module for mcmicro

Overview repository on IMC data analysis

Reproducible Data Science environments for R with Nix

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

Code used to benchmark Xenium

dalmatian is a collection of high-level companion functions for Firecloud and FISS.

Repository containing all the scripts and the models used for the analysis

Code used to benchmark Xenium

IDEIS is a software for CD45 isoform detection in single-cell data.

Mixed-effect model to test differences in cell type proportions from single-cell data, in Python

The R Installation Manager

scPCA is a versatile matrix factorisation framework designed to analyze single-cell data across multiple conditions.

Pick colours from an image in R

A list of alternatives for Adobe software

Compute generation probabilities of CDR3 amino acid and nucleotide sequences

The code for running the analysis component of CSI-Microbe

A template for standard compliant snakemake-workflows

Python interface to running command-line and web-based MHC binding predictors

An R package for tidyverse-friendly statistical inference

Weakly supervised learning uncovers phenotypic signatures in single-cell data

Personalised HLA mapping for scRNA and bulkRNA sequencing data

Positron, a next-generation data science IDE

This is the repository for the code used in my dissertation, for tidied code, please view https://github.com/RcwYuen/TCR-Embeddings

Highly informative TCR representation model