Methods for decontamination of single cell data

Accelerated genomics workflows in NextFlow

A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.

Generate masks for scRNA-seq clusters on t-SNE or UMAP plots

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

Workflow for the Association of T-cell receptors from 3' single-cell RNA-seq (WAT3R)

Framework for sensitive DE testing (using neighbourhoods)

RStudio Server in a Singularity container

nextflow ATACseq pipeline for GG02

Deep probabilistic analysis of single-cell and spatial omics data

nextflow RNAseq pipeline for GG02

The statistical language R compiled to WebAssembly via Emscripten, for use in web browsers and Node.

A curated collection of Nextflow implementation patterns

Interpretation of cell states using reference single-cell maps

argon dashboard template

GitHub Actions for the R community

A minimalistic router for your Shiny apps.

Assertive programming for R analysis pipelines

Microsoft's Fluent UI for Shiny apps

An interactive explorer for single-cell transcriptomics data

Benchmarking analysis of data integration tools

A toolkit for QC and visualization of ATAC-seq results.

R package implementation of Milo for testing for differential abundance in KNN graphs

A Shiny web app for visualizing genomic data from brain tumors in 3D.

Peer-to-peer hypermedia protocol

A command line interface for interacting with the Box API.

Nextflow training material for introductory tutorial

Portable WDL workflows for IDseq production pipelines