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1. beef-exudate-metabolomics beef-exudate-metabolomics Public

   Unravelling novel metabolites in beef exudate to ensure meat freshness and safety. An untargeted LC-MS/MS metabolomics pipeline for detecting microbial spoilage in beef, comparing a conventional de…

   Python 1 2

2. catharanthus-rnaseq-pipeline catharanthus-rnaseq-pipeline Public

   RNA-seq analysis pipeline for Catharanthus roseus across six tissues, highlighting terpenoid indole alkaloid (TIA) biosynthesis. Includes read alignment, quantification, and differential expression…

   Shell 2 2

3. seurat-pbmc3k-SingleCellAnalysis-walkthrough seurat-pbmc3k-SingleCellAnalysis-walkthrough Public

   Annotated Seurat v5 walkthrough of the 10x Genomics PBMC 3k dataset: QC, normalization, feature selection, PCA, graph-based clustering, UMAP, marker discovery, and annotation of 2,638 cells into 8 …

   R 1

4. atac-seq-cancer-pipeline atac-seq-cancer-pipeline Public

   Reproducible bulk ATAC-seq pipeline for chromatin accessibility in cancer: Bowtie2 alignment, stringent filtering (duplicates, chrM, ENCODE blacklist, MAPQ 30), MACS2 peak calling, FRiP and TSS-enr…

   Shell 1

5. Camelina-sativa-gene-expression-analysis Camelina-sativa-gene-expression-analysis Public

   Jupyter Notebook 1

6. multiomics_data_integration_Malus_domestica multiomics_data_integration_Malus_domestica Public

   R 1 1