Here we highlight software that was developed by Van Galen Lab members and collaborators.

Accompanying paper: Griffin et al, Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin, Nature, 2023.

Code for analysis of single-cell gene expression and genotyping data. See also vangalenlab resources website and GEO repository.

Accompanying paper: Miller et al, Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations, Nat Biotechnol, 2022.

Developed by Caleb Lareau, the maegatk package processes .bam files with mitochondrial reads to generate high-quality heteroplasmy estimation from sequencing data.

We developed a table of mitochondrial variants, their effects on the resultant proteins, and the potential functional consequences to assess the potential beneficial/detrimental consequences of mutations.

Various scripts used to analyze the data and generate figures for the paper.

Accompanying paper: DePasquale et al, Single-cell Multiomics Reveals Clonal T-cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm, Frontiers in Immunology, 2022.

This is a pipeline to process data generated by the protocol T-cell Receptor Enrichment to linK clonotypes by sequencing (TREK-seq). See also WATR paper.

Various scripts used to analyze the data and generate figures for the paper.

Accompanying paper: Van Galen et al, Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity, Cell, 2019.

This repository contains the original code, largely written by Volker Hovestadt.

Scripts that facilitate the visualization of genes of interest in barplots, violin/sina plots, and heatmaps.