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1. ML_analysis ML_analysis Public

   A reproducible multi-omics machine-learning workflow for MDS classification. The workflow integrates DNA methylation, gene expression, and mutation or clinical features, creates a stratified train/…

   Python

2. RNA_seq_analysis RNA_seq_analysis Public

   A reproducible bulk RNA-seq workflow for adapter trimming, rRNA depletion, STAR alignment, gene-level quantification, DESeq2 differential expression, and preranked GSEA.

   Shell

3. Single_cell_analysis Single_cell_analysis Public

   A reproducible single-cell RNA-seq workflow for quality control, normalization, highly variable gene selection, PCA, graph-based clustering, k-means clustering, UMAP/t-SNE visualization, marker dis…

   R

4. ChIP_seq_analysis ChIP_seq_analysis Public

   A reproducible, sample-sheet-driven ChIP-seq workflow for paired-end sequencing data.

   Shell

5. ERRBS_analysis ERRBS_analysis Public

   A reproducible ERRBS methylation workflow for adapter trimming, Bismark alignment, cytosine extraction, methylation summarization, and differential methylation analysis.

   Shell

6. Proteomics_analysis Proteomics_analysis Public

   A reproducible, dual-entry proteomics pipeline. The Nextflow entry point supports: DDA or DIA.

   Python