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).
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Has reproduction · 73
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.
PMID 31110304 · PMC6527554 · Scientific reports · 2019 · 8 claims · 7 setups
GREIN is a web application providing user-friendly interfaces to manipulate, visualize, and analyze GEO RNA-seq data.
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Has reproduction · 95
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.
PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups
transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms
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Has reproduction · 88
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.
PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups
COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.
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Has reproduction · 53
PulmonDB: a curated lung disease gene expression database.
PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 6 claims · 6 setups
PulmonDB is a curated, web-based gene expression database and R package integrating microarray and RNA-seq data for COPD and IPF with manually curated controlled-vocabulary annotation.
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Has reproduction · 65
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.
PMID 33932985 · PMC8088074 · BMC bioinformatics · 2021 · 8 claims · 5 setups
SPEAQeasy is a portable, easy-to-install, Nextflow-powered RNA-seq processing pipeline that lowers the computational entry barrier for biologists/clinicians
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Has reproduction · 38
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.
PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups
A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).
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Has reproduction · 90
Inferring a spatial code of cell-cell interactions across a whole animal body.
PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups
cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells
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Has reproduction · 76
GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.
PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups
GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place
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Has reproduction · 50
Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.
PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups
A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database