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).

• GoMiner: a resource for biological interpretation of genomic and proteomic data.

  PMID 12702209 · PMC154579 · Genome biology · 2003 · 8 claims · 4 setups

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  GoMiner organizes 'interesting' gene lists (e.g., differentially expressed genes) into the Gene Ontology hierarchy for biological interpretation, displaying results as both a tree and a directed acyclic graph (DAG).

  du145 gene gominer cdna flow category

• Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

  PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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  A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

  pca malignant tcga mda single-cell infercnv pseudotime

• pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.

  PMID 31114675 · PMC6505635 · F1000Research · 2019 · 7 claims · 4 setups

  Has reproduction · 90

  pysradb provides a command-line interface to query metadata and download raw sequencing data from NCBI SRA using the SRAdb SQLite database.

  sra-deposited pc3 sra tissues metadata polya assays