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ppromprasert/README.md

Patharapa "Candy" Promprasert

Bioinformatics Scientist | Cancer Genomics • Multi-Omics • Translational Oncology

Bioinformatics analyst working across cancer genomics, transcriptomics, epigenomics, single-cell analysis, population genomics, and clinical outcomes. My work focuses on building reproducible computational analyses that connect molecular tumor states with disease biology, patient characteristics, and translational hypotheses.

Featured research

HNSC Mitochondrial Adaptive Tumor State

Multi-cohort analysis integrating TCGA-HNSC survival modeling, SLC25A10/SFXN3/SGPP1 expression states, immune and stromal deconvolution, transcriptome-wide pathway analysis, GSE65858 external survival validation, and GSE164690 single-cell cross-scale validation.

Methods: R, Cox PH, Kaplan-Meier, limma, CIBERSORT, ESTIMATE, GSEA, Seurat, inferCNV, patient-level pseudobulk

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OED → OSCC Epigenomic Progression

Illumina EPIC methylation analysis integrating baseline lesion definitions, grade-adjusted limma modeling, repeated-measures handling, known OSCC biology, CosMx-derived spatial candidates, exposure-associated methylation signatures, and longitudinal lesion trajectories.

Methods: Illumina EPIC, limma, duplicateCorrelation, beta/M values, BH-FDR, longitudinal analysis, spatial multi-omics integration

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Thyroid Cancer Multi-Omics

Integrated somatic DNA and RNA analysis of thyroid cancer incorporating variant QC, driver-event characterization, BRAF/RAS/TERT biology, differential expression, clinical disease status, inflammatory programs, and pathway-level interpretation.

Methods: GATK, Funcotator, maftools, DESeq2, R, Bash, Linux/HPC

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CRC Population Genomics & Genetic Ancestry

Population-genomics workflow using RNA-derived germline variants, 1000 Genomes references, PLINK PCA, supervised/unsupervised ADMIXTURE, and missingness sensitivity.

Methods: nf-core, GATK HaplotypeCaller, bcftools, PLINK, ADMIXTURE, R, Bash, Slurm

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Technical focus

Languages: R, Python, Bash
Genomics: GATK, bcftools, samtools, VEP, ANNOVAR, maftools, GISTIC2
Transcriptomics: DESeq2, limma, Salmon, GSEA
Single-cell: Seurat, Harmony, Azimuth, SingleR, Monocle3, inferCNV
Epigenomics: Illumina EPIC, sesame, EpiDISH, duplicateCorrelation
Population genomics: PLINK, ADMIXTURE, SNPRelate
Compute: Linux, Slurm, Nextflow/nf-core, Conda, Singularity/Apptainer

Pinned Loading

  1. hnsc-mats-multicohort hnsc-mats-multicohort Public

    Multi-cohort HNSCC analysis of a three-gene mitochondrial adaptive tumor state using survival modeling, immune deconvolution, pathway analysis, external validation, and scRNA-seq.

    R

  2. oed-oscc-epigenomic-progression oed-oscc-epigenomic-progression Public

    EPIC methylation analysis of OED-to-OSCC progression integrating grade-adjusted modeling, spatial candidates, exposure-associated signatures, and longitudinal lesion trajectories.

    R

  3. thyroid-cancer-multiomics thyroid-cancer-multiomics Public

    Integrated thyroid cancer DNA/RNA analysis of somatic drivers, MAPK and TERT alterations, disease-associated transcriptomics, inflammasome biology, demographic associations, and staged multi-omics …

    R

  4. cms4-singlecell-cnv-ancestry cms4-singlecell-cnv-ancestry Public

    Single-cell inferCNV analysis of CMS4 colorectal cancer evaluating CNV burden, clonal diversity, chromosome/gene-level architecture, and African-ancestry stratification.

    R

  5. crc-population-genomics-ancestry crc-population-genomics-ancestry Public

    Population-genomics workflow for CRC using RNA-derived germline variants, 1000 Genomes, PLINK PCA, supervised/unsupervised ADMIXTURE, and missingness sensitivity.

    Shell

  6. cms4-singlecell-immune-states-ancestry cms4-singlecell-immune-states-ancestry Public

    CMS4 CRC single-cell immune-state analysis integrating Seurat, Harmony, Azimuth, pseudobulk DESeq2, pathway GSEA, and African ancestry.

    R