The 30 Days of Python programming challenge is a step-by-step guide to learn the Python programming language in 30 days. This challenge may take more than 100 days. Follow your own pace. These vide…

Video+code lecture on building nanoGPT from scratch

Creating beautiful plots of data maps

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

Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms

Systematically learn and evaluate manifolds from high-dimensional data

Demultiplexing pooled scRNA-seq data with or without genotype reference

Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.

Python package to find communication-driven intercellular flows from single-cell RNA-sequencing and spatial transcriptomics data.

SingleCell Nanopore sequencing data analysis

Starter repository for submissions to the CausalBench challenge for gene-gene graph inference from genetic perturbation experiments.

Demultiplexing and debarcoding tool designed for LR-Split-seq data.

Management of remote Jupyter sessions

Tools for single-cell feature barcoding analysis

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