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).

• MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

  PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

  Has reproduction · 24

  MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

  environmental quality-filtered assembled predicted metagenomic metagenome gene

• MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

  PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups

  Has reproduction · 50

  MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.

  bovine simulated cami trimming decontamination assembly

• COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.

  PMID 19958500 · PMC2788389 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  COMUS is a bioinformatics system for detecting and depositing new mutations from patient DNA with a clinician-friendly interface

  ab1 fasta mutation hemophilia base-calling sequence known-variant

• RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

  PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 66

  RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.

  microbial reconstructed synthetic real shotgun ssu full-length

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

  PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 67

  Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

  anas duck million random illumina read novo

• 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

• SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

  PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

  embryonic hesc small sequence adapter

• transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.

  PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups

  Has reproduction · 95

  transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms

  piper assembled longum predicted rna-seq novo transcriptome

• 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

  Has reproduction · 38

  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).

  gossypium uppermost root reads bulk leaf rt-qpcr

• QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

  PMID 36699347 · PMC9722223 · Bioinformatics advances · 2022 · 6 claims · 8 setups

  Has reproduction · 78

  QuasiFlow is a Nextflow pipeline that runs entirely locally via command-line tools and a local HIVdb database copy to analyze NGS-based HIV-1 drug resistance testing data.

  hiv-1 same paired-end reads ngs-based concordance read

• Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

  PMID 24211736 · PMC3969109 · Methods (San Diego, Calif.) · 2014 · 8 claims · 6 setups

  Has reproduction · 71

  The 'hyb' pipeline detects, calls, folds and annotates chimeric reads from CLASH high-throughput sequencing data.

  ago1 test clash multiplexed clash benchmarking demultiplexing

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript