Software & Packages

Genomics software

MPRA barcode–element mapping

A pipeline for mapping barcodes to elements from long-read Nanopore sequencing of MPRA libraries. The repository documents its configuration, dependencies, and output tables; it is currently tailored to a specific plasmid configuration.

View the public repository

In development

MSF

An algorithm for fast querying of similar sequences. The repository is currently private.

ZiPert

Software for differential gene expression analysis in Perturb-seq data using zero-inflated models. The repository is currently private.

Earlier research and study code

• Quantum kernel investigation: notebooks exploring kernel regression and dimension reduction.
• Binary dimension reduction: earlier code repository.
• Convex optimization: earlier code repository.

See my GitHub profile for all public repositories and the Blog & Archive for related notes.