A Python package using Gromov-Wasserstein distance to compare cell shapes

Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA

Minimum-distortion embedding with PyTorch

Personal notes about work- and coding-related topics

Set of useful functions for handling spatial genomics data

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

Analyses from the manuscript, "Single cell spatial transcriptomic profiling of childhood-onset lupus nephritis reveals complex interactions between kidney stroma and infiltrating immune cells"

An R-based interface for loom files

R to Fortran Transpiler

Lightweight extension of the base R graphics system

🧭 Navigate single-cell RNA-seq datasets in your web browser.

AnnData interoperability in R

reticulate-free single cell format conversion

Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.

Probabilistic cell segmentation for in situ spatial transcriptomics

GLMMs with adaptive Gaussian quadrature

Fast Wilcoxon and auROC

ClusterMap for multi-scale clustering analysis of spatial gene expression

Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.

flexplot: graphical data analysis

Code used to carry out parameter estimation, correlation estimation, type 1 error analysis, and power analysis for our "Pseudoreplication in Single-Cell" study

CosMx Spatial Molecular Imager-derived cell profiles to aid in cell typing of SMI data.

Bayesian Segmentation of Spatial Transcriptomics Data

R package for image processing

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also…

Dimensionality reduction in very large datasets using Siamese Networks