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).

• hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.

  PMID 36498841 · PMC9738810 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  hgtseq is a fully automated, portable, and scalable Nextflow/nf-core pipeline for detecting horizontal gene transfer signatures from unmapped sequencing reads.

  copd chikv bos canis exome taxonomic reference

• Eduomics: a Nextflow pipeline to simulate -omics data for education.

  PMID 41816779 · PMC12972896 · NAR genomics and bioinformatics · 2026 · 8 claims · 4 setups

  Full-text index only

  Eduomics is a Nextflow DSL2 pipeline that automates generation of validated variant-calling and RNA-seq datasets for education while abstracting away technical requirements

  chromosome full simulated exome rna-seq pipeline

• Application of qualifying variants for genomic analysis.

  PMID 41570118 · PMC12926777 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 4 setups

  Full-text index only

  QVs should be treated as dynamic, multifaceted elements permeating the entire analysis workflow, not as a single static filtering step

  in-house hapmap3 genome framework exome gwas wgs

• Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

  PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction

  Tree-based (XGBoost, LightGBM) and deep-learning (TabNet) tabular ML classifiers achieve state-of-the-art somatic vs germline classification in tumor-only WES samples, outperforming PureCN.

  tcga same metastatic tumor-only whole-exome wes copy-number