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🧭 Navigate single-cell RNA-seq datasets in your web browser.
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)
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) Try the below web server!
A shortcut to your favorite code
Python package to find communication-driven intercellular flows from single-cell RNA-sequencing and spatial transcriptomics data.
llama3 implementation one matrix multiplication at a time
Methods to discover gene programs on single-cell data
R package implementation of Milo for testing for differential abundance in KNN graphs
Systematically learn and evaluate manifolds from high-dimensional data
Break your chain at the cursor line. Run the first bit. See the output. Be free.