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    26 repositories

    • proseg-workflow

      Public
      Proseg nextflow pipeline for Cirro
      Nextflow
      •0•2•3•0•Updated May 7, 2025May 7, 2025

    • kompot

      Public
      Differential abundance and gene expression in single-cell data
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 7, 2025May 7, 2025

    • Palantir

      Public
      Single cell trajectory detection
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •52•0•0•1•Updated May 2, 2025May 2, 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

    • ArchR

      Public
      ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
      R
      •
      MIT License
      •144•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • 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•9•3•0•Updated Apr 23, 2025Apr 23, 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

    • atac_metacell_utilities

      Public
      Snakemake pipeline for scATAC metacell utilities such as primed and lineage specific scores, chromVAR, in-silico ChIP
      Python
      •0•5•1•3•Updated Mar 21, 2025Mar 21, 2025

    • Mellon

      Public
      Non-parametric density inference for single-cell analysis.
      single-cellgaussian-processesdensity-estimationcell-differentiationdifferentiable
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•69•2•0•Updated Mar 12, 2025Mar 12, 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
      •29•1•0•0•Updated Dec 2, 2024Dec 2, 2024

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.5k•0•0•0•Updated Nov 30, 2024Nov 30, 2024

    • kdpeak

      Public
      A kernel density estimation based peak caller
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 23, 2024Jul 23, 2024

    • ecosystem-packages

      Public
      Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •49•0•0•1•Updated May 14, 2024May 14, 2024

    • benchmarkDA

      Public
      Differential Abundance benchmarks
      HTML
      •1•0•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
      •98•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
      •629•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

    • conda-forge-staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5.3k•0•0•0•Updated Jun 20, 2023Jun 20, 2023

    • wot

      Public
      A software package for analyzing snapshots of developmental processes
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •34•0•0•0•Updated Mar 28, 2023Mar 28, 2023

    • getspan

      Public
      Gene trend regression and span identification
      Jupyter Notebook
      •0•0•0•0•Updated Oct 11, 2022Oct 11, 2022

    • jupyter-rsession-proxy

      Public
      Jupyter extensions for running an RStudio rsession proxy
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •88•0•0•0•Updated Apr 21, 2022Apr 21, 2022

    • SeqGL

      Public
      SeqGL is a group lasso based algorithm to extract TF sequence signals from ChIP, DNase and ATAC-seq profiles
      R
      •6•0•0•0•Updated Mar 4, 2021Mar 4, 2021

    • Harmony

      Public
      Harmony framework for connecting scRNA-seq data from discrete time points
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •13•0•0•0•Updated Mar 2, 2021Mar 2, 2021

    • wishbone

      Public
      Wishbone is an algorithm to align cells along developmental trajectories with branches
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •35•0•0•0•Updated May 14, 2020May 14, 2020