R / DESeq2
Open repository
RNA-seq Workflow
End-to-end DEG workflow with count data, metadata, QC, DESeq2 analysis, PCA, heatmaps, volcano plot, result tables, and a short interpretation report.
Selected work
Alternative Splicing Notes
A public rMATS skipped-exon analysis example with event filtering and candidate review notes.
Open repositoryGEMsplice HumanGEM Alzheimer Analysis
Curated Alzheimer/control workflow integrating Salmon quantification outputs, Human-GEM resources, GEMsplice/iMAT-style scripts, summary tables, figures, and final report structure.
Open repositoryHuman-GEM GIMME Alzheimer Analysis
Context-specific AD and control models from Salmon quantification outputs, with precomputed results, QC reports, and figures.
Open repositorySynthetic splicing and pathogenicity iMAT showcase
Three computed iMAT layers for 200 artificial samples, with downloadable matrices, statistics tables, and input audits.
Open the results showcaseiMAT Tool
Interactive terminal tool for per-sample Human-GEM iMAT, Fisher and reporter-like analysis, and optional gene zeroing, with a synthetic demo.
Open projectBioinformatics Portfolio Projects
Sequence alignment, FASTA utilities, motif search, volcano plotting, variant summaries, and interactive R/Shiny exploration examples.
Open repositorySynthetic data, computed with Gurobi
Three-stage iMAT demo on synthetic data
Follow 200 artificial samples through Human-GEM 1.12.0, COBAMP reaction scoring, TROPPO iMAT with Gurobi, and Fisher plus reporter-like statistics. The showcase includes all three reaction matrices, four vector figures, and the checks behind them.
- Three 13,070 × 200 reaction activity matrices
- Matched model-size and reaction-overlap checks
- Four inspectable vector figures
- Fisher and reporter-like result tables
- Documented synthetic inputs and reproducible scripts
A reproducible methods demonstration using synthetic inputs. No biological or clinical conclusion is drawn from these figures.
100 samples per group or stage
Example results
RNA-seq workflow
Differential expression volcano plot
Portfolio figure showing differential expression signal across genes, prepared as part of a reproducible RNA-seq workflow.
Example output from public dataset.
RNA-seq QC
Sample distance heatmap
Quality-control style output for reviewing sample relationships before interpretation.
Example output from public dataset.
RNA-seq figures
Top DEG heatmap
Expression-pattern figure prepared for selected differentially expressed genes.
Example output from public dataset.
GEMsplice / iMAT
Pathway-level relative flux change
Advanced portfolio output comparing Alzheimer and control groups across pathway-level metabolic flux changes.
Public RNA-seq source: PRJNA670209 (SRR12850842, SRR12850850–54; 3 AD, 3 control samples).
Objective projections
Pairwise objective review
Projection panels showing how sample groups separate across selected metabolic objective values.
Public RNA-seq source: PRJNA670209 (SRR12850842, SRR12850850–54; 3 AD, 3 control samples).
HumanGEM tx2gene
Curated pathway scatter
Pathway-level scatter plot from the HumanGEM tx2gene analysis.
Public RNA-seq source: PRJNA670209 (SRR12850842, SRR12850850–54; 3 AD, 3 control samples).
Featured synthetic iMAT run
Reaction activity across three model stages
All 100 samples in each group or stage are shown. The same control vectors are used throughout the staged comparison.
Synthetic-data methods demonstration. Open full results and downloads.
Paired model comparison
Model-size changes by sample
Each artificial AD-labelled sample is paired with its own splicing and rank-adjusted model.
Synthetic-data methods demonstration; no disease inference.
Portfolio outputs are shown for research-support demonstration only. Clinical diagnosis, treatment decisions, and patient-specific interpretation are outside the service scope.