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).

• EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.

  PMID 34805989 · PMC8598301 · NAR genomics and bioinformatics · 2021 · 8 claims · 5 setups

  Has reproduction · 54

  EpiDiverse Toolkit provides Nextflow-based pipelines for WGBS mapping, methylation calling, variant calling, differential methylation, and EWAS tailored to non-model plant ecology

  populus nigra genome variant clustering

• Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

  PMID 42054377 · PMC13127959 · PloS one · 2026 · 8 claims · 7 setups

  Full-text index only

  Integrating prothoracic ganglion RNAseq data with the draft genome refines gene predictions, adding 3,868 novel genes and 9,172 new transcript isoforms (including non-coding transcripts)

  bimaculatus prothoracic differentially gbig rna-seq genome differential

• ScLRTC: imputation for single-cell RNA-seq data via low-rank tensor completion.

  PMID 34844559 · PMC8628418 · BMC genomics · 2021 · 8 claims · 8 setups

  Has reproduction · 85

  scLRTC imputes dropout entries closest to the original expression values on simulated datasets, outperforming other state-of-the-art methods by SSE and PCC.

  usoskin pollen zeisel yan scrna-seq umap masking