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1. tle3-multiomics-NI2024 tle3-multiomics-NI2024 Public

   Multiomics analysis code for Tle3 study — RNA-seq, ATAC-seq, CUT&RUN (Nature Immunology, 2024)

   R

2. nextflow-bio-tutorials nextflow-bio-tutorials Public

   Step-by-step Nextflow DSL2 tutorials for bioinformatics: channels, QC, RNA-seq, variant calling, proteomics, scatter-gather, and container integration

   Nextflow

3. proteomics-dea-bmd-pipeline proteomics-dea-bmd-pipeline Public

   End-to-end proteomics workflow for QC, differential abundance analysis, and benchmark-dose modeling

   R

4. ATACseq_pipeline_diffbind ATACseq_pipeline_diffbind Public

   Reproducible ATAC-seq pipeline for BAM preprocessing, MACS3 peak calling, and differential accessibility analysis using DiffBind. Includes QC, consensus peak generation, and identification of diffe...

   Python

5. tcga-depmap-drug-profiler tcga-depmap-drug-profiler Public

   Digital patient generation and drug response prediction via TCGA-DepMap integration — CVAE virtual patients, multi-level similarity scoring, 578-compound drug profiling

   R

6. xenium-giotto-template xenium-giotto-template Public template

   Reusable Giotto Suite workflow template for 10x Genomics Xenium spatial transcriptomics data.

   R