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).

• Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.

  PMID 41486154 · PMC12828970 · BMC bioinformatics · 2026 · 8 claims · 8 setups

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  Frag'n'Flow is a Nextflow-based pipeline that encapsulates FragPipe, automating manifest/workflow generation, tool dependency management, and downstream analysis for HPC/cloud/cluster environments.

  laboratory institutional breast pluripotent ram cpu storage

• Integrative network modeling reveals mechanisms underlying T cell exhaustion.

  PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 7 setups

  Has reproduction · 59

  TCE arises from changes in diverse gene regulatory interactions across a shared network rather than dysregulation of a single gene

  cd8+ tce manual gene principal

• scDenorm: a denormalization tool for integrating single-cell transcriptomics data.

  PMID 41915012 · PMC13142155 · GigaScience · 2026 · 8 claims · 7 setups

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  Inconsistent delta-method normalization across datasets introduces biases (e.g., B-cell separation) that persist even after integration with Harmony, scanorama, or BBKNN.

  10x brain ucsc datasets scrna-seq integration snrna-seq

• A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.

  PMID 42111187 · PMC13157187 · iScience · 2026 · 8 claims · 8 setups

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  cfDNAanalyzer integrates feature extraction, feature processing/selection, and machine learning model building into a single one-command-line toolkit for cfDNA genomic sequencing data

  balanced breast healthy multi-cancer cfdna machine computational

• Development of a pediatric immune cell atlas and characterization of CD4+ T cells in food allergy.

  PMID 42025535 · PMC13105851 · Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology · 2026 · 8 claims · 8 setups

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  A pediatric single-cell PBMC reference atlas was developed from 57 healthy children across 8 public scRNA-seq studies.

  pbmcs cd3+ cd4+ memory scrna-seq pseudobulk bulk