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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)
KMulder-IGR / sopa
Forked from gustaveroussy/sopaTechnology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
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