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).

• nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

  PMID 36961337 · PMC10199315 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups

  Has reproduction · 88

  nf-core/isoseq is a new automated Nextflow-based pipeline that processes raw Iso-Seq subreads through to genome annotation (BED format) without requiring transcriptome assembly.

  organism-specific iso-seq reference mapped pacbio subread long-read

• SEAseq: a portable and cloud-based chromatin occupancy analysis suite.

  PMID 35193506 · PMC8864840 · BMC bioinformatics · 2022 · 7 claims · 2 setups

  Has reproduction · 94

  SEAseq is a comprehensive, infrastructure-independent pipeline that performs the major analyses needed to process ChIP-Seq/CUT&RUN chromatin binding datasets in a single execution

  any chip-seq cut&run

• Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

  PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

  Full-text index only

  Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

  encode genome cdna-to-genome novo comparative