Case Studies
Inspect real biological analyses produced with Pipette’s agentic bioinformatics platform — including source data, methods, findings, limitations, provenance artifacts, figures, and downloadable session reports.
HepG2 Drug-Perturbation Proteomics: Mechanism-of-Action Analysis of 172 Compounds
Batch-aware analysis of 1,232 HepG2 DIA-MS samples across 172 drugs and 8,630 proteins, with response signatures, exploratory pathway analysis, and explicit RedMix confounding.
RNA-Seq Differential Expression: Rice Salt-Alkali Stress
Full pipeline from paired-end FASTQ to differential expression at two timepoints (Day 1 & Day 5). 12 samples, 3,456 DEGs, volcano plots, heatmaps, and enrichment-ready gene lists.
Single-Cell Clustering & Marker Identification: Human Pancreatic Islets
Scanpy analysis of 3,072 CEL-seq2 cells from four donors. After QC, 2,681 cells formed 18 Leiden clusters with marker-supported working annotations and explicit artifact flags.
Differential Expression: Dexamethasone-Treated Airway Smooth Muscle Cells
Cell-line-aware DESeq2 analysis of 8 airway smooth muscle samples. Of 22,369 tested genes, 4,000 passed FDR < 0.05; the case study includes PCA, artifacts, and interpretation limits.
KRAS Variant Analysis & Survival Outcomes in PDAC
Observational Kaplan–Meier and pairwise Cox analysis of G12D, G12V, G12R, and KRAS wild type in a 2,034-patient comparison cohort—with conflicting report denominators disclosed.
Lung Cancer Tumor-Microenvironment Literature Scan
Report-derived themes from a 10-paper scan spanning single-cell and spatial studies. The case study explicitly flags the missing citation registry, search string, and inconsistent date ranges.
Revised FOXP2 Protein Comparison Across 15 Vertebrates
Curated sequence comparison using a full 772-column MAFFT alignment: 94.0% conserved positions and two reported human-specific sites. Revised results are separated from the stale legacy body retained in the PDF.
Rett Syndrome Variant Frequencies Across ClinVar and gnomAD
Revised allele-specific matching of 586 Rett-associated pathogenic or likely pathogenic variants: 493 absent, 92 ultra-rare, and one rare, with unresolved API and structural-variant cases disclosed.
Imatinib Docking Against an AlphaFold ABL1 Model
Compound retrieval, rule-based ADMET, fpocket selection, and rigid-receptor Vina docking. The −9.4 kcal/mol score is presented as a ranking heuristic—not validated affinity or potency.