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1. rnaseq_klebsiella_pipeline rnaseq_klebsiella_pipeline Public

   A complete bioinformatics pipeline (FastQC, fastp, HISAT2, featureCounts, DESeq2) for RNA-Seq DGE analysis of Klebsiella pneumoniae (WT vs. ΔcpxR).

   Jupyter Notebook 4

2. project_variant_calling project_variant_calling Public

   Bioinformatics pipeline (GATK/BWA/SnpEff) to identify antibiotic resistance mutations (DAP/VAN) in Staphylococcus aureus.

   Jupyter Notebook 4

3. Mtb_Genomic_Analysis- Mtb_Genomic_Analysis- Public

   A bioinformatics pipeline (SPAdes, Prokka, Roary) to identify novel PAS resistance SNPs in M. tuberculosis.

   Jupyter Notebook 3

4. 16S_microbiome_analysis_crohns_disease 16S_microbiome_analysis_crohns_disease Public

   End-to-end 16S microbiome analysis (FASTQ to PCoA) of Crohn's Disease. Implements a QIIME 2 & Docker pipeline to identify significant phylogenetic dysbiosis (p=0.0007).

   Jupyter Notebook 3

5. mdr-pa-genomic-epidemiology mdr-pa-genomic-epidemiology Public

   A reproducible Snakemake pipeline for the high-throughput genomic epidemiology of 96 MDR P. aeruginosa strains (BioProject PRJNA771342).

   Jupyter Notebook 2

6. Shotgun_Metagenomics_Analysis Shotgun_Metagenomics_Analysis Public

   Shotgun metagenomics analysis pipeline for Type 2 Diabetes gut microbiome using Snakemake.

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