Repositories list

• MetaSRA-pipeline

  Public
  MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

  natural-language-processingtext-miningdata-mining+ 7bioinformaticsrna-seqbiologybiomedical-informaticsannotation-processorontologiesentity-matching

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •14•45•265•1•Updated Oct 3, 2025Oct 3, 2025

• RSEM

  Public
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

  C++

  •

  GNU General Public License v3.0

  •125•454•131•9•Updated Mar 13, 2024Mar 13, 2024

• MetaSRA-API-backend

  Public
  MetaSRA API + website back-end

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Dec 5, 2023Dec 5, 2023

• MetaSRA-website-frontend

  Public
  MetaSRA: normalized metadata for the Sequence Read Archive

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•5•0•Updated Dec 5, 2023Dec 5, 2023

• CellO

  Public
  CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

  machine-learningbioinformaticsrna-seq+ 6computational-biologyontologiescell-type-classificationsingle-cell-rna-seqcell-biologycell-type

  Jupyter Notebook

  •

  MIT License

  •14•67•7•4•Updated Jul 8, 2023Jul 8, 2023

• cell-type-classification-paper

  Public
  Code implementing experiments described in "Hierarchical cell type classification using mass, heterogeneous RNA-seq data from human primary cells"

  Python

  •1•5•1•0•Updated Jul 10, 2020Jul 10, 2020

• deweylab.github.io

  Public
  The deweylab website

  HTML

  •0•1•0•0•Updated Sep 30, 2016Sep 30, 2016

• detonate

  Public
  DETONATE: DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

  C++

  •4•13•7•0•Updated Jun 22, 2016Jun 22, 2016