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1. nextflow-ngs-pipelines nextflow-ngs-pipelines Public

   Nextflow DSL2 pipelines for NGS analysis: population genomics (ADMIXTURE/PCA/FST), WES variant calling (GATK), scRNA-seq integration (Harmony), bulk RNA-seq DE + GSEA.

   Python

2. adna-nextflow-pipeline adna-nextflow-pipeline Public

   Nextflow DSL2 pipeline for ancient DNA: raw fastq to EIGENSTRAT via PALEOMIX, damage-aware clipping, pseudo-haploid genotyping and Rx sex determination (horse, EquCab3.0).

   Python

3. YOLO-classification-for-PKA-SPARK YOLO-classification-for-PKA-SPARK Public

   YOLO11 detection and classification of PKA-SPARK biosensor responding cells in fluorescence microscopy. Class accuracy 0.932 ± 0.074 by leave-one-frame-out cross-validation.

   Jupyter Notebook