Use Cases

See how researchers use Pipette for real-world genomics analyses — from a single prompt to publication-ready results.

Rice RNA-seq DESeq2 HISAT2 fastp

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.

Team Pipette
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Human scRNA-seq Scanpy Leiden UMAP

Single-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.

Team Pipette
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Human RNA-seq DESeq2 R

Differential 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.

Team Pipette
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Human PDAC KRAS Survival Analysis cBioPortal Kaplan-Meier

KRAS 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.

Team Pipette
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Human Lung Cancer scRNA-seq Tumor Microenvironment PubMed Literature Review

PubMed 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.

Team Pipette
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