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    36 repositories

    • kompot

      Public
      Differential abundance and gene expression in single-cell data
      Python
      •
      GNU General Public License v3.0
      •1•8•0•0•Updated Jul 28, 2026Jul 28, 2026

    • anndata

      Public
      Annotated data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •206•0•0•7•Updated Jul 28, 2026Jul 28, 2026

    • Mellon

      Public
      Non-parametric density inference for single-cell analysis.
      single-cellgaussian-processesdensity-estimation
      single-cellgaussian-processesdensity-estimationcell-differentiationdifferentiable
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •5•75•2•0•Updated Jul 28, 2026Jul 28, 2026

    • fh-hpc-skills

      Public
      Claude Code skills for effective HPC usage.
      0•1•0•0•Updated Jul 24, 2026Jul 24, 2026

    • spatial-smooth

      Public
      Composable spatial and cell-state smoothing of gene signatures for single-cell and spatial transcriptomics
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 22, 2026Jul 22, 2026

    • atac_metacell_utilities

      Public
      Snakemake pipeline for scATAC metacell utilities such as primed and lineage specific scores, chromVAR, in-silico ChIP
      Python
      •0•6•0•3•Updated Jun 22, 2026Jun 22, 2026

    • scEcho

      Public
      A statistical framework for identifying desynchronized cell states and their driver genes/regulatory elements from paired single-cell RNA and ATAC data.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Jun 15, 2026Jun 15, 2026

    • convert2anndata

      Public
      An R package to convert SingeCellExperiment and Seurat objects into anndata as comprehensively as possible.
      R
      •
      GNU General Public License v3.0
      •2•14•3•1•Updated May 19, 2026May 19, 2026

    • kompot_benchmarkDA

      Public
      benchmarkDA repo for Kompot
      HTML
      •0•0•0•1•Updated Apr 11, 2026Apr 11, 2026

    • claude-code-markdowns

      Public
      0•0•0•0•Updated Mar 20, 2026Mar 20, 2026

    • Palantir

      Public
      Single cell trajectory detection
      Jupyter Notebook
      •
      MIT License
      •65•0•0•1•Updated Mar 5, 2026Mar 5, 2026

    • kompot_notebooks

      Public
      Notebooks used to make plots for the kompot paper.
      Jupyter Notebook
      •0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • kompot_scaling

      Public
      Memory and runtime scaling of kompot.
      Jupyter Notebook
      •0•0•0•0•Updated Dec 5, 2025Dec 5, 2025

    • kompot_de_benchmark

      Public
      Differential expression stability benchmark for Kompot.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 5, 2025Dec 5, 2025

    • ecosystem-packages

      Public
      Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •84•0•0•2•Updated Nov 26, 2025Nov 26, 2025

    • Harmony

      Public
      Harmony framework for connecting scRNA-seq data from discrete time points
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •15•0•0•0•Updated Nov 22, 2025Nov 22, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •4k•0•0•0•Updated Nov 21, 2025Nov 21, 2025

    • link_plot

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Sep 5, 2025Sep 5, 2025

    • proseg-workflow

      Public
      Proseg nextflow pipeline for Cirro
      Nextflow
      •0•3•4•0•Updated Jul 29, 2025Jul 29, 2025

    • ArchR

      Public
      ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
      R
      •
      MIT License
      •160•0•0•0•Updated Jul 24, 2025Jul 24, 2025

    • kdpeak

      Public
      A kernel density estimation based peak caller
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 1, 2025Jul 1, 2025

    • single-cell-primers

      Public
      Primers for single-cell data analysis
      Jupyter Notebook
      •
      MIT License
      •2•5•0•1•Updated May 1, 2025May 1, 2025

    • worm-glia-atlas

      Public
      Repository for tutorials and reproducibility notebooks for the worm glia scRNA-seq atlas
      Jupyter Notebook
      •1•0•0•1•Updated Mar 25, 2025Mar 25, 2025

    • mellon-feedstock

      Public
      A conda-smithy repository for mellon.
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • SEACells

      Public
      SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •35•1•0•0•Updated Dec 2, 2024Dec 2, 2024

    • benchmarkDA

      Public
      Differential Abundance benchmarks
      HTML
      •2•1•0•1•Updated May 10, 2024May 10, 2024

    • 2for1separator

      Public
      Deconvolve CUT&Tag 2for1 data.
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Apr 22, 2024Apr 22, 2024

    • signac

      Public
      R toolkit for the analysis of single-cell chromatin data
      R
      •
      Other
      •106•0•0•0•Updated Feb 28, 2024Feb 28, 2024

    • scanpy

      Public
      Single-cell analysis in Python. Scales to >1M cells.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •760•0•0•0•Updated Sep 25, 2023Sep 25, 2023

    • MellonReproducibility

      Public
      Notebooks for reproducing figures in the Mellon manuscript
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jun 24, 2023Jun 24, 2023
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