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    38 repositories

    • Baysor

      Public
      Bayesian Segmentation of Spatial Transcriptomics Data
      segmentationbayesianspatial-transcriptomics
      segmentationbayesianspatial-transcriptomicsxenium
      Julia
      •
      MIT License
      •40•204•38•1•Updated Apr 20, 2026Apr 20, 2026

    • leidenAlg

      Public
      Implements the Leiden algorithm via an R interface
      C
      •4•12•1•0•Updated Apr 16, 2026Apr 16, 2026

    • clone2vec

      Public
      Repository for the clone2vec python package
      Python
      •0•15•0•0•Updated Apr 10, 2026Apr 10, 2026

    • sccore

      Public
      Core utilities for single-cell RNA-seq
      R
      •3•13•1•0•Updated Apr 6, 2026Apr 6, 2026

    • conos

      Public
      R package for the joint analysis of multiple single-cell RNA-seq datasets
      scrna-seqsingle-cell-rna-seqbatch-correction
      scrna-seqsingle-cell-rna-seqbatch-correction
      R
      •
      GNU General Public License v3.0
      •39•224•8•1•Updated Apr 1, 2026Apr 1, 2026

    • pagoda2

      Public
      R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
      scrna-seqtranscriptomicssingle-cell
      scrna-seqtranscriptomicssingle-cellsingle-cell-rna-seq
      JavaScript
      •47•252•2•0•Updated Apr 1, 2026Apr 1, 2026

    • N2R

      Public
      R extensions to N2 implementing approximate nearest neighbor search methods
      C++
      •3•10•1•0•Updated Mar 31, 2026Mar 31, 2026

    • cacoa

      Public
      Single-cell Case Control Analysis
      R
      •12•56•10•1•Updated Feb 26, 2026Feb 26, 2026

    • scistreer

      Public
      R/Rcpp implementation of the ScisTree algorithm
      evolutionphylogeneticssingle-cell
      evolutionphylogeneticssingle-cell
      R
      •
      GNU General Public License v3.0
      •3•7•0•0•Updated Feb 4, 2026Feb 4, 2026

    • numbat

      Public
      Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
      cancer-genomicssingle-cellphylogeny
      cancer-genomicssingle-cellphylogenysingle-cell-rna-seqsingle-cell-analysissingle-cell-atac-seqcnv-detectionsingle-cell-omicsspatial-transcriptomicslineage-tracing
      R
      •
      Other
      •33•214•80•1•Updated Feb 4, 2026Feb 4, 2026

    • cellAdmix

      Public
      Jupyter Notebook
      •
      MIT License
      •4•30•7•7•Updated Jan 22, 2026Jan 22, 2026

    • thymus-mesenchyme

      Public
      Code and notebooks for Gustafsson et al. scRNA-Seq analysis of thymic mesenchymal cells
      Jupyter Notebook
      •0•1•1•0•Updated Nov 5, 2025Nov 5, 2025

    • clonal-atlas-paper

      Public
      The repository with the code and analysis for the paper [Erickson et al]
      Jupyter Notebook
      •0•3•0•0•Updated Jun 5, 2025Jun 5, 2025

    • cellAdmix-Notebooks

      Public
      Jupyter Notebook
      •
      MIT License
      •0•7•2•0•Updated Apr 23, 2025Apr 23, 2025

    • GraphPriorKMeans

      Public
      Julia
      •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • cellAdmix-preprint

      Public
      Evaluating and correcting cell admixtures in imaging-based spatial transcriptomics data
      Jupyter Notebook
      •
      Other
      •2•1•1•0•Updated Sep 25, 2024Sep 25, 2024

    • gpsFISH

      Public
      Optimization of gene panels for targeted spatial transcriptomics
      R
      •
      Other
      •2•7•3•0•Updated Jul 16, 2024Jul 16, 2024

    • scITD

      Public
      Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
      R
      •4•64•7•0•Updated Apr 14, 2024Apr 14, 2024

    • hahmmr

      Public
      Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq
      R
      •
      Other
      •0•13•2•0•Updated Apr 2, 2024Apr 2, 2024

    • conosViz

      Public
      Shiny App to Visualize Dendrograms and Heatmaps from Conos
      R
      •1•2•0•0•Updated Nov 4, 2022Nov 4, 2022

    • cacoaAnalysis

      Public
      Analysis for the Cacoa paper
      R
      •1•3•0•0•Updated Aug 25, 2022Aug 25, 2022

    • NumbatAnalysis

      Public
      Analysis scripts and notebooks for Numbat paper
      R
      •
      MIT License
      •0•10•2•0•Updated Aug 12, 2022Aug 12, 2022

    • dropEst

      Public
      Pipeline for initial analysis of droplet-based single-cell RNA-seq data
      pipelinescrna-seqpreprocessing
      pipelinescrna-seqpreprocessingsingle-cell-rna-seq
      C++
      •
      GNU General Public License v3.0
      •42•95•40•1•Updated Jun 22, 2022Jun 22, 2022

    • vrnmf

      Public
      Volume-regularized NMF
      R
      •4•18•0•0•Updated Apr 14, 2022Apr 14, 2022

    • AllenBrain_AnnData

      Public
      Instructions on how to convert Allen Brain Atlas data into AnnData files
      Python
      •0•2•1•0•Updated Mar 21, 2022Mar 21, 2022

    • drat

      Public
      Drat repo with R packages
      0•1•0•0•Updated Feb 12, 2022Feb 12, 2022

    • BaysorAnalysis

      Public
      Analysis for the Baysor paper
      Jupyter Notebook
      •
      MIT License
      •2•7•3•1•Updated Dec 4, 2021Dec 4, 2021

    • ScisTree

      Public
      Cell tree inference and genotype calling from noisy single cell data
      C++
      •
      Other
      •2•1•0•0•Updated Nov 17, 2021Nov 17, 2021

    • slideseqde

      Public
      R
      •0•0•0•0•Updated Nov 15, 2021Nov 15, 2021

    • mouseCochlea

      Public
      processing code for Tasdemir-Yilmaz et al. "Diversity of developing peripheral glia revealed by single cell RNA sequencing"
      HTML
      •0•0•0•0•Updated Oct 13, 2021Oct 13, 2021
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