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Starred repositories
A ready-to-go template for building powerful Agent APIs
Calculate the carbon footprint of Nextflow workflows from execution traces!
Example python scripts for snRNAseq processing
A reproducible RNA-seq analysis pipeline using Snakemake and R. Includes quality control, alignment, quantification, differential expression, and statistical visualization.
A flexible pipeline for complete analysis of bacterial genomes
A nextflow workflow / pipeline to perform common NGS read preprocessing. This can be used as stand-alone or can be used as subworkflow in another nextflow pipeline.
Scripts and workflow for 16S rRNA microbiome analysis from fecal samples, including preprocessing, denoising, taxonomy assignment and visualization.
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Updated Sep 23, 2025
A modest re-desing update for the classic FastQC report.
Logging of scripts suitable for clinical trials
Evaluation and polishing workflows for T2T genome assemblies
A pipeline for extracting Presence-Absence Variations (PAVs) in eukaryotic and prokaryotic genomes across multiple assemblies.
Improving RNA structure prediction through multitask learning on diverse crowdsourced data.
A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
Assessing the quality of metagenome-derived genome bins using machine learning
A minimal, responsive, and feature-rich Jekyll theme for technical writing.
PandaDock: A Physics-Based Molecular Docking using Python
Batch Correction and Adaptive Contrast Calling in Complex RNA-seq Experimental Designs Using DESeq2
Visualizing nearest neighbors of high-dimensional samples
Quick mapping of Uniprot sequences to PDB structures
ARG normalization by mapping to the ARO ontology.
SemiBin: metagenomics binning with self-supervised deep learning