ShinyCell2 is a lightweight R package for building interactive, shareable apps to explore single-cell multi-omics, scATAC-seq and spatial transcriptomics data with customizable, publication-ready v…

An R package for visualising cell-cell interactions

A Toolbox for Spatial Transcriptomics Analysis

R package to describe the morphological variations and create "morphotypes" from greyscale images

A revival of a 20th century interwar typeface.

Easy to use encryption tools for R

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

Test genes for Spatial Variation

PICAFlow: a complete R workflow dedicated to flow/mass cytometry data, from data pre-processing to deep and comprehensive analysis.

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data

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

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

A microbiome analysis toolkit for R

Bitmap and Vector font rendering

R6 based utilities for 3D meshes.

Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.

The integration of single cell rank-based gene set enrichment analysis

The R package of 'Scalable Two-level Spatial Clustering for Integrative Analysis of Multi-sample SRT Data'

NicheNet: predict active ligand-target links between interacting cells

Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms

AUCell: score single cells with gene regulatory networks

Combination matrix axis for 'ggplot2' to create 'UpSet' plots

This repository contains math tutorials I created for Bioinformatics and Computational Biology.

TRAjectory-based Differential Expression analysis for SEQuencing data

single cell Flux Estimation Analysis (scFEA)

A shortcut to your favorite code

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