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).

• Skittle: a 2-dimensional genome visualization tool.

  PMID 20042093 · PMC2817707 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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  Skittle is a 2D genome visualization tool combining a color-coded Nucleotide Display, a Repeat Map, a Repeat Overview, and an Alignment Cylinder to reveal genomic patterns at multiple scales

  chromosome random alpha genome nucleotide repeat alignment

• 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

• An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.

  PMID 15005801 · PMC341449 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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  An XML schema called Annotated Gel Markup Language (AGML) is proposed to manage, analyze, and disseminate annotated 2D gel electrophoresis and MS results.

  biological 2de agml gel mass visualization

• Identifying repeat domains in large genomes.

  PMID 16507140 · PMC1431705 · Genome biology · 2006 · 7 claims · 5 setups

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  A repeat domain graph, built using a modified A-Bruijn graph framework, decomposes a repeat library into shared repeat domains and reveals the mosaic structure of repeat families.

  repbase elegans concatenated repeat comparative dot

• miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

  PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

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  miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

  conserved putative mirna-target normal comparative machine mirna