Open-source bioinformatics software, workflows, and infrastructure I have developed.
nf-core / Nextflow
A workflow for preprocessing mass spectrometry–based metabolomics data, including MS1 quantification and MS2-based identification.
Nextflow
A metabolomics preprocessing workflow for iterative parameter optimization using internal standards and repeated sample injections.
R package
Rapid metabolite identification from MS1 and MS2 data, including adduct estimation, neutral-mass estimation, and spectrum merging.
A workflow using miRanda and RNAhybrid to identify candidate miRNA targets.
Circadian analysis
Mixed-model differential circadian-rhythm analysis for RNA-seq, methylation, metabolomics, proteomics, and other data types.
Cloud infrastructure
Infrastructure for deploying Kubernetes clusters to run Nextflow-based workflows.
R / Kubernetes
A lightweight wrapper for offloading R sessions to Kubernetes.
Pathway analysis
Pathway-level multi-modal integration using p-value fusion for modalities with KEGG pathway mappings.
Scalable computation
Methods for calculating dissimilarity matrices on large datasets using multicore execution with a controlled memory footprint.