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1. tcga-brca-rnaseq-degs-ml tcga-brca-rnaseq-degs-ml Public

   End-to-end RNA-seq pipeline on TCGA-BRCA (213 samples): DESeq2 differential expression, clusterProfiler functional enrichment, and ML-based biomarker ranking (Random Forest, LASSO, SVM) achieving >…

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2. srr25083113-genome-assembly-annotation srr25083113-genome-assembly-annotation Public

   De novo genome assembly and structural annotation of bacterial isolate SRR25083113 using SPAdes, Prodigal, Barrnap, and ARAGORN — a macOS ARM–compatible pipeline alternative to QUAST/Prokka.

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3. hisat2-bowtie2-alignment-comparison hisat2-bowtie2-alignment-comparison Public

   R-based comparison of HISAT2 vs Bowtie2 alignment performance across RNA-Seq and WGS applications using chr21 reference and platform-representative simulated data; includes MAPQ-based SAM quality a…

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4. ngs-platform-quality-comparison ngs-platform-quality-comparison Public

   R-based quality comparison of Illumina HiSeq 2500 vs NovaSeq 6000 using authentic NCBI SRA metadata and platform-representative simulated reads; reports Q20/Q30, GC content, and per-base quality me…

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