Use Cases
See how researchers use Pipette for real-world genomics analyses — from a single prompt to publication-ready results.
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.
View Session ReportSingle-Cell Clustering & Marker Identification: Human Pancreatic Islets
Standard QC, clustering, and marker gene identification on 1,432 cells. 10 distinct clusters, 941 marker genes (top: TTR, INS, PPY), UMAP visualisations, and heatmaps — completed in 82 seconds.
View Session ReportDifferential Expression: Dexamethasone-Treated Airway Smooth Muscle Cells
DESeq2 analysis of dexamethasone vs control across 8 samples (4 cell lines). 4,000 DEGs (2,193 up, 1,807 down), volcano plots, heatmaps, and PCA showing 71% variance explained — completed in 53 seconds.
View Session ReportKRAS Variant Analysis & Survival Outcomes in PDAC
KRAS variant distribution and Kaplan-Meier survival analysis on 2,034 PDAC patients from MSK 2024. G12D (42.5%), G12V (33.6%), G12R (16.7%) with significant survival differences (p<0.0001) — completed in 41 seconds.
View Session ReportPubMed Literature Review: scRNA-seq in Lung Cancer Tumor Microenvironment
Automated PubMed search and synthesis of 10 recent papers on single-cell RNA-seq analysis of lung cancer TME. Key themes: T cell exhaustion, macrophage reprogramming, and novel biomarkers (TCF1, CXCL16+, PPP1R13L) — completed in 7 seconds.
View Session ReportFOXP2 — The Language Gene: Protein Comparative Analysis Across Mammals and Birds
This report presents a comparative analysis of the FOXP2 protein across 15 representative vertebrate species (mammals and birds), correcting methodology issues identified in the first version. Key improvements: fragment sequences replaced or excluded, full alignment used without aggressive trimming, and identity calculations verified on gapless pairwise positions.
View Session ReportRett Syndrome ClinVar Variants & Population Frequency Analysis
Automated analysis of pathogenic and likely pathogenic MECP2 variants from ClinVar with gnomAD population frequency annotation.
View Session ReportImatinib (Gleevec) — BCR-ABL Kinase Inhibitor Drug Design Analysis
Complete computational drug design pipeline: PubChem compound retrieval, ADMET profiling, AlphaFold structure fetch, fpocket binding site detection, and AutoDock Vina molecular docking — confirming Imatinib as a strong BCR-ABL binder at -9.4 kcal/mol.
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