hypergeometric testing of guide RNA identity to assign cell barcodes to a guide identity

A mapper for 10x-flex single cell sequencing reads with fixed abstract geometries

A flexible package manager that supports multiple versions, configurations, platforms, and compilers.

A conda-smithy repository for nvim.

A conda-smithy repository for neovim.

Parsing HTML at the command line

Transforming Foundation Model Representations for OOD Data

BulkFormer: A large-scale foundation model for human bulk transcriptomes

Data analysis for the scBaseCount manuscript

LLM agents for working with the SRA and associated bioinformatics databases.

Reproducible figure generation, data, and methods for the Spatial Atlas of Human Anatomy (SAHA) project.

A grammar of graphics for comparative genomics

VariantFormer: A hierarchical transformer integrating DNA sequences with genetic variations

Definition and DDLs for the OMOP Common Data Model (CDM)

Server for Squeezebox and compatible players. This server is also called Lyrion Music Server.

Apache Iceberg

BAyesian Model-Building Interface (Bambi) in Python.

Cytograph version used for adult human-brain analysis

Code used for RNAseq analysis in "A dynamic fibroblast response shapes wound healing after brain injury," Ewing-Crystal et al.

scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images

Analysis code from "Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states"

A minimalist design exploration