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ParthDoshi97/README.md

Hi, I'm Parth Doshi 👋

Bioinformatics Analyst · Genomics & Multi-Omics · NGS Pipelines · Python / R

🧬 MSc Applied Bioinformatics graduate from Cranfield University with 3+ years of freelance bioinformatics experience and prior molecular diagnostics exposure.

I turn complex genomic, transcriptomic, metagenomic, epigenomic, and multi-omics datasets into reproducible workflows, clear biological interpretation, and publication-ready reports.

🚀 Featured Projects

Project What it does
vcf_annatation_raredisease Nextflow DSL2 pipeline for rare-disease variant annotation & prioritization (VEP, vcfanno, Genmod)
tcga-brca-rnaseq-wgcna TCGA breast-cancer RNA-seq: DESeq2 + WGCNA co-expression networks
vcf-liftover-wrapper High-throughput clinical VCF liftover engine (GRCh37 ⇄ GRCh38) in Rust
AMR-GeneDetection-ResFinder-CARD Antimicrobial-resistance gene detection using ResFinder + CARD
Sake_Fermentation_Predictive_modeling Predictive modeling of sake fermentation outcomes

🛠️ Skills

Languages: Python · R · Bash · SQL NGS/Genomics: WGS/WES · GATK · nf-core/Sarek · SAMtools/BCFtools · VEP · gnomAD Transcriptomics: DESeq2 · edgeR/limma · STAR/HISAT2 · Salmon · clusterProfiler Workflow/Cloud: Nextflow · Snakemake · Docker · Singularity · HPC · AWS · GCP

📫 Connect

LinkedIn Email Upwork

📄 Publication: Glycosylated Antibiotics: New Promising Bacterial Efflux Pumps Inhibitors — MRJI, 2024

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  1. AMR-GeneDetection-ResFinder-CARD AMR-GeneDetection-ResFinder-CARD Public

    This repository hosts powerful scripts designed to predict antimicrobial resistance genes using the Resfinder and CARD (Comprehensive Antibiotic Resistance Database) databases. Tailored for high-th…

    Shell 1

  2. tcga-brca-rnaseq-wgcna tcga-brca-rnaseq-wgcna Public

    RNA-seq differential expression and data visualization pipeline for TCGA-BRCA, including DESeq2, enrichment analysis, WGCNA modules, and hub-gene discovery.

    R

  3. NHANES_diabetes_biostatistics_ML NHANES_diabetes_biostatistics_ML Public

    Diabetes risk factors in NHANES: survey-weighted stats meets machine learning

    Jupyter Notebook

  4. Survival_Analysis Survival_Analysis Public

    This project performs a survival analysis on the flchain dataset from the survival R package to investigate the relationship between serum free light chain (FLC) levels and all-cause mortality.

    HTML

  5. vcf-liftover-wrapper vcf-liftover-wrapper Public

    Rust

  6. vcf_annatation_raredisease vcf_annatation_raredisease Public

    This repository is a Nextflow DSL2 pipeline for rare disease variant annotation and prioritization from an already-called VCF.

    Python