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Software
Open-source tools from the lab, newest first. Each links to its code repository and the publication it accompanies; parentheses list the lab members among the authors.
CLADES↗2026
Contrastive learning for differential splicing, using orthologous positive pairs.
integrateCNV↗2026
Infers copy-number alterations from snRNA-seq paired with matched bulk whole-exome sequencing.
PICASSO↗2026
Phylogenetic inference of cell clones and clonal phylogenies from noisy single-cell CNA profiles.
PLASTRO↗2026
Plasticity analysis for paired lineage-tracing and phenotypic data.
Manify↗2025
Python library for learning and analyzing data in non-Euclidean (product-manifold) spaces.
Hyperbolic embeddings of genomic sequence.
SEACells↗2023
Aggregates single cells into interpretable metacells for scRNA-seq and scATAC-seq.
MiSDEED↗2022
Synthetic-data engine for microbiome study power analysis and study design.
CoPTR↗2022
Infers personalized microbial growth rates from metagenomic coverage (peak-to-trough ratios).
Recovery algorithm and pooling designs for one-stage noisy group testing under a probabilistic model.
LUMINATE↗2020
Denoises longitudinal microbiome data; infers relative abundances and separates biological from technical zeros.
Models microbial community dynamics in the simplex of relative abundances.
DyStruct↗2019
Infers population structure from time-series (ancient-DNA) genotype data.