Single-Cell Genomics |

Arc Institute scverse Satellite Workshop

Sat, 01 Nov 2025 00:00:00 +0000

scverse Conference 2025

Sat, 01 Nov 2025 00:00:00 +0000

PerTurbo

Sun, 01 Sep 2024 00:00:00 +0000

PerTurbo is a scalable Bayesian analysis framework for large-scale Perturb-seq screens, with a GPU-accelerated implementation of the probabilistic model using PyTorch, Pyro, and Lightning.

See the associated manuscript, A scalable Bayesian analysis method for large single cell CRISPR screens (in preparation).

IGVF Consortium CRISPR Screen Pipeline

Sat, 01 Jun 2024 00:00:00 +0000

Co-led construction of an end-to-end Nextflow pipeline for reproducibility analysis of consortium-scale single-cell CRISPR screen datasets, as part of the consortium CRISPR Focus Group.

See the associated manuscript, A unified end-to-end pipeline for reproducibility analysis of consortium-scale single-cell CRISPR screen datasets (in preparation).

MEGATRON

Thu, 01 Jun 2023 00:00:00 +0000

MEGATRON (MEGA TRajectories of clONes) supports single-cell lineage tracing analysis using mitochondrial mutations, developed to refine computational strategies for tracking clonal dynamics in single-cell data.

scDNA Analysis Pipeline

Tue, 01 Jan 2019 00:00:00 +0000

Pipelines for calling copy number variants, structural variants, and single nucleotide variants from single-cell whole genome sequencing data, developed during my time at the Dana-Farber Cancer Institute.