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1. bioinformatics-portfoliobioinformatics-portfolioPublic

   A bioinformatics portfolio showcasing variant analysis, single-cell RNA-seq, and spatial transcriptomics pipelines

   Python 2

2. scATAC-WNN-multimodalscATAC-WNN-multimodalPublic

   R 1

3. crispr-mageck-screencrispr-mageck-screenPublic

   MAGeCK CRISPR screen hit-calling + clusterProfiler enrichment on a real published pooled screen (Wang et al. 2014)

   R

4. cutandrun-pipelinecutandrun-pipelinePublic

   bowtie2 + MACS3 peak calling (Snakemake DAG, SLURM profile) on public CUT&Tag data -- honest CUT&RUN/CUT&Tag disclosure

   Python

5. nf-variant-pipelinenf-variant-pipelinePublic

   Germline variant-calling pipeline (BWA/GATK/bcftools) in Nextflow, with Docker/Singularity profiles — security-reviewed

   Nextflow

6. perturb-seq-deep-learningperturb-seq-deep-learningPublic

   PyTorch classifier predicting CRISPRi guide identity from single-cell expression (Adamson et al. 2016 Perturb-seq)

   Python