Stars
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
scPCA is a versatile matrix factorisation framework designed to analyze single-cell data across multiple conditions.
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
Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
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
Methods to discover gene programs on single-cell data
R extension library for rust designed to be familiar to R users.