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).

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.

  PMID 37247570 · PMC10878300 · Ticks and tick-borne diseases · 2023 · 7 claims · 3 setups

  Full-text index only

  The MPAS pipeline is a portable, reproducible Nextflow-based bioinformatics pipeline that identifies and summarizes amplicon sequences produced by the MPAS assay.

  host-seeking mpas same targeted mpas clc

• nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

  PMID 36961337 · PMC10199315 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups

  Has reproduction · 88

  nf-core/isoseq is a new automated Nextflow-based pipeline that processes raw Iso-Seq subreads through to genome annotation (BED format) without requiring transcriptome assembly.

  organism-specific iso-seq reference mapped pacbio subread long-read

• SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

  PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

  Full-text index only

  EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

  genome affymetrix probe database microarray interactive

• An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

  PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

  Full-text index only

  Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

  private disease uniprot snps database controlled sequence

• A workflow reproducibility scale for automatic validation of biological interpretation results.

  PMID 37150537 · PMC10164546 · GigaScience · 2022 · 8 claims · 4 setups

  Has reproduction · 100

  Comparing output files by checksum alone is insufficient to verify reproducibility, since checksums can differ even when the underlying biological interpretation is unchanged

  nf-core sam vcf workflow checksum biological workflow

• WASP: a versatile, web-accessible single cell RNA-Seq processing platform.

  PMID 33736596 · PMC7977290 · BMC genomics · 2021 · 7 claims · 7 setups

  Has reproduction · 59

  WASP is a software platform for processing Drop-Seq-based scRNA-seq data generated with ddSEQ or 10x protocols, combining a Snakemake pre-processing pipeline with an R Shiny post-processing application.

  specified generic scrna-seq read reference

• Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

  PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups

  Full-text index only

  PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.

  subset drosophila ensembl lc-ms icat peptide-to-genome

• Rfam 15: RNA families database in 2025.

  PMID 39526405 · PMC11701678 · Nucleic acids research · 2025 · 8 claims · 6 setups

  Has reproduction · 68

  Rfamseq was expanded to 26 106 genomes, a 76% increase, by incorporating the latest UniProt reference proteomes and additional viral genomes

  rfamseq rfam hepatitis mirbase covariance structure covariation

• Curation of over 10 000 transcriptomic studies to enable data reuse.

  PMID 33599246 · PMC7904053 · Database : the journal of biological databases and curation · 2021 · 8 claims · 6 setups

  Has reproduction · 80

  Gemma is a curated database and bioinformatics system that addresses metadata, probe annotation, and expression data inconsistencies in GEO to enable transcriptomic data reuse

  microarray curated geo microarray rna-sequencing probe-to-gene

• poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.

  PMID 34394197 · PMC8355734 · Frontiers in genetics · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  poreCov is an easy-to-use, fast, and robust Nextflow-based workflow for reference-based SARS-CoV-2 genome reconstruction and lineage determination from nanopore sequencing data

  porecov sars-cov-2 nanopore fastq gisaid workflow real-world

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

  Full-text index only

  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome

• An extensive evaluation of read trimming effects on Illumina NGS data analysis.

  PMID 24376861 · PMC3871669 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Read trimming increases the quality and reliability of downstream NGS analyses (RNA-Seq mapping, SNP identification, genome assembly) while reducing execution time and computational resources.

  homo arabidopsis prunus saccharomyces rna-seq snp novo

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• A Bioinformatics Workflow to Identify eccDNA Using ECCFP From Long-Read Nanopore Sequencing Data.

  PMID 41924242 · PMC13037781 · Bio-protocol · 2026 · 7 claims · 5 setups

  Has reproduction · 100

  ECCFP significantly improves eccDNA detection sensitivity, accuracy, and runtime efficiency compared to other pipelines

  nanopore trimmed aligned base sequencing adapter

• Proteomics data repositories.

  PMID 19795424 · PMC2908408 · Proteomics · 2009 · 5 claims · 5 setups

  Full-text index only

  The YRC Public Data Repository (YRC PDR) provides a single unified interface disseminating multi-technology proteomics data (mass spectrometry, yeast two-hybrid, fluorescence microscopy, structure prediction) linked to protein annotations from many source databases.

  multi-organism yeast proteomes cerevisiae tandem yeast fluorescence