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).

• 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

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of >1054 single-cell experiments (>4 million cells) from mouse and human across many tissues and platforms.

  grch38 homogeneous per single single-cell clustering cell-type

• MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.

  PMID 29901703 · PMC6025204 · GigaScience · 2018 · 6 claims · 7 setups

  Has reproduction · 95

  A two-step 'omni' RNA-seq pipeline (MetaMap) combining STAR human alignment with CLARK-S metagenomic classification can quantify archaeal, bacterial, and viral reads from the non-human read fraction of human RNA-seq data

  clinical hela tumor rutkowski bulk dual negative

• DFAST and DAGA: web-based integrated genome annotation tools and resources.

  PMID 27867804 · PMC5107635 · Bioscience of microbiota, food and health · 2016 · 8 claims · 7 setups

  Has reproduction · 89

  DFAST is a web-based bacterial genome annotation and DDBJ submission pipeline with integrated CheckM quality assessment and ANI taxonomic assessment.

  lactobacillus genomes representative raw genome ortholog average

• VGEA: an RNA viral assembly toolkit.

  PMID 34567846 · PMC8428259 · PeerJ · 2021 · 8 claims · 5 setups

  Has reproduction · 80

  VGEA is a Snakemake workflow that chains existing tools (fastp, BWA, SAMtools, IVA, shiver, SeqKit, QUAST, MultiQC) into an all-in-one RNA viral genome assembly pipeline

  sars-cov-2 lassa hiv-1 ngs-based computational comparative

• 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

• ChimerDB 2.0--a knowledgebase for fusion genes updated.

  PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

  Full-text index only

  ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

  genbank sra pubmed transcript-to-genome ngs literature

• GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.

  PMID 35501696 · PMC9063052 · BMC bioinformatics · 2022 · 6 claims · 3 setups

  Has reproduction · 67

  GEMmaker, an nf-core compliant Nextflow workflow, can quantify gene expression from small to massive RNA-seq datasets while remaining reproducible via versioned containerized software.

  oryza arabidopsis generic rna-seq workflow

• 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

• CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification.

  PMID 36304334 · PMC9580850 · Frontiers in bioinformatics · 2022 · 8 claims · 5 setups

  Has reproduction · 88

  CIRCprimerXL is a high-throughput, user-friendly circRNA RT-qPCR primer design pipeline available as both a web tool and a standalone Nextflow/Docker pipeline

  synthetic sw480 circrnas rt-qpcr circrna primer

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

  four raw orthologous mammalian whole-genome novo homology-based