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    15 repositories

    • DANIO_ReCODE_scRNAseq_workshop_2026

      Public
      Single cell transcriptomics training for the DANIO-ReCODe Doctoral Network, 2026
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 16, 2026Jun 16, 2026

    • EISCA_training_course

      Public
      This repository contains the data and tutorials for single-cell analysis using EISCA.
      0•0•0•0•Updated Jun 12, 2026Jun 12, 2026

    • HELMSLEY_Crohn_scRNA-Seq

      Public
      scRNA-Seq analysis of fibrostenosing Crohn's disease
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 9, 2026Mar 9, 2026

    • GeneSpectra

      Public
      GENE classification and cross-SPECies comparison of cell Types with single cell RNA-seq data
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • GeneSpectra_reproducibility

      Public
      Scripts and notebooks which generated results in the GeneSpecira preprint
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • BENGAL

      Public
      Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets
      Python
      •
      GNU General Public License v3.0
      •9•43•4•0•Updated Jul 20, 2025Jul 20, 2025

    • GeneSpectraKG

      Public
      Biocypher KG for GeneSpectra results
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 24, 2025Jun 24, 2025

    • scGOclust

      Public
      Gene ontology terms to compare single cell RNA-seq data
      R
      •
      GNU General Public License v3.0
      •0•11•1•0•Updated May 6, 2025May 6, 2025

    • CATD_snakemake

      Public
      Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq datasets
      snakemakepipelinedeconvolution
      snakemakepipelinedeconvolutionsingle-cell-rna-seqdeconvolution-methodscell-type-abundance
      R
      •
      GNU General Public License v3.0
      •3•16•2•0•Updated Apr 28, 2025Apr 28, 2025

    • scGOclust_reproducibility

      Public
      Notebooks and files from the scGOclust study
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • GBC_SUM159PT_paper

      Public
      R
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Feb 2, 2025Feb 2, 2025

    • GBC_SUM159PT_paper_figures

      Public
      R
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • BENGAL_reproducibility

      Public
      BENchmark inteGrAtion strategies for cross-species anaLysis of single cell RNA sequencing data
      Jupyter Notebook
      •
      MIT License
      •0•5•0•0•Updated Jan 17, 2024Jan 17, 2024

    • CATD_reproducibility

      Public
      Notebooks and scripts for reproducing CATD paper
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 11, 2024Jan 11, 2024

    • scOntoMatch

      Public
      scOntoMatch is an R package which unifies ontology annotation of scRNA-seq datasets to make them comparable across studies
      HTML
      •
      Other
      •0•11•0•0•Updated Oct 27, 2023Oct 27, 2023
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