Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• scSurv: a deep generative model for single-cell survival analysis.

  PMID 41429574 · PMC12797213 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  scSurv combines a Cox proportional hazards model with a deep generative model (VAE) of single-cell transcriptomes to estimate individual cellular contributions to clinical outcomes

  simulated tcga melanoma renal scrna-seq bulk single-cell

• CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data.

  PMID 41231245 · PMC13053056 · Cancer research · 2026 · 7 claims · 7 setups

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  CanSig is a comprehensive benchmarking tool for evaluating computational methods that identify shared transcriptional signatures in cancer from scRNA-seq data

  neftel kim scrna-seq same scrna-seq ground-truth robustness

• spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.

  PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups

  Has reproduction · 53

  spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data

  bistable three-gene emt circuits simulation mixed-state grn

• Robust and efficient annotation of cell states through gene signature scoring.

  PMID 41708334 · PMC12951948 · Genome research · 2026 · 8 claims · 8 setups

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  Established scoring methods (Seurat, SCANPY, UCell, JASMINE) fail to provide robust and comparable score distributions across diverse signatures and experimental conditions, precluding accurate unsupervised cell-state annotation.

  pbmc colorectal esophageal crc scrna-seq cross-implementation signature