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).

• L2L: a simple tool for discovering the hidden significance in microarray expression data.

  PMID 16168088 · PMC1242216 · Genome biology · 2005 · 8 claims · 4 setups

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  L2L systematically compares a user's differentially expressed gene list against a database of published differentially expressed gene lists to find statistically significant overlaps and generate hypotheses about shared mechanisms

  mammalian user-supplied diabetic uniprot compiled l2l re-analysis

• DupyliCate: mining, classifying, and characterizing gene duplications.

  PMID 42209743 · PMC13219399 · Scientific reports · 2026 · 8 claims · 8 setups

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  DupyliCate is a Python tool for identifying and classifying gene duplication arrays, using BUSCO-based species-specific thresholds and offering integrated expression divergence and Ka/Ks analysis.

  arabidopsis thaliana brassicales phytozome sequence duplication runtime

• iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data.

  PMID 35899080 · PMC9310080 · NAR genomics and bioinformatics · 2022 · 8 claims · 4 setups

  Has reproduction · 58

  iCOMIC provides a GUI-driven, Snakemake-based pipeline integrating multiple tools for DNA-Seq and RNA-Seq analysis with minimal command-line interaction.

  giab monocyte missense somatic germline rna-seq machine

• BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

  PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

  pre-selected pre-tabulated genes ranked kegg expression text-mining

• MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.

  PMID 36386613 · PMC9651917 · Frontiers in microbiology · 2022 · 7 claims · 4 setups

  Has reproduction · 83

  MetaGT is a pipeline that combines metatranscriptomic and metagenomic data from the same sample to assemble complete transcript sequences

  simulated mock16 real snailgut novo transcript gene

• MILANO--custom annotation of microarray results using automatic literature searches.

  PMID 15661078 · PMC547913 · BMC bioinformatics · 2005 · 7 claims · 4 setups

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  MILANO annotates microarray gene lists by counting literature co-occurrences of each gene with user-defined secondary terms

  well-known list over-producing known medline generif microarray

• 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

• Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.

  PMID 34911933 · PMC8674326 · Nature communications · 2021 · 8 claims · 7 setups

  Has reproduction · 79

  Low-grade (Gleason pattern 3) prostate cancer cells share chromatin accessibility features that are lost in high-grade (Gleason pattern 4) tumours

  flash-frozen tcga single differentially single-cell bulk topic

• miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.

  PMID 34308351 · PMC8294687 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction

  miRge3.0 is a Python 3-based small RNA-seq and tRF analysis pipeline that improves on miRge2.0 (which was Python 2.7-based)

  sra synthetic qiagen-processed same small umi mirna