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  1. pagoda2 pagoda2 Public

    R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

    JavaScript 241 47

  2. conos conos Public

    R package for the joint analysis of multiple single-cell RNA-seq datasets

    R 217 39

  3. Baysor Baysor Public

    Bayesian Segmentation of Spatial Transcriptomics Data

    Julia 201 39

  4. numbat numbat Public

    Haplotype-aware CNV analysis from single-cell RNA-seq

    R 200 28

  5. dropEst dropEst Public

    Pipeline for initial analysis of droplet-based single-cell RNA-seq data

    C++ 95 42

  6. scITD scITD Public

    Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition

    R 62 4

Repositories

Showing 10 of 38 repositories
  • cacoa Public

    Single-cell Case Control Analysis

    kharchenkolab/cacoa’s past year of commit activity
    R 52 11 10 1 Updated Dec 19, 2025
  • thymus-mesenchyme Public

    Code and notebooks for Gustafsson et al. scRNA-Seq analysis of thymic mesenchymal cells

    kharchenkolab/thymus-mesenchyme’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Nov 5, 2025
  • cellAdmix Public
    kharchenkolab/cellAdmix’s past year of commit activity
    Jupyter Notebook 7 MIT 0 0 0 Updated Oct 24, 2025
  • numbat Public

    Haplotype-aware CNV analysis from single-cell RNA-seq

    kharchenkolab/numbat’s past year of commit activity
    R 200 28 78 1 Updated Oct 22, 2025
  • scLiTr Public

    Repository for the scLiTr (single-cell Lineage Tracing analysis) python package

    kharchenkolab/scLiTr’s past year of commit activity
    Python 13 0 0 0 Updated Oct 5, 2025
  • pagoda2 Public

    R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

    kharchenkolab/pagoda2’s past year of commit activity
    JavaScript 241 47 1 (1 issue needs help) 0 Updated Aug 18, 2025
  • clonal-atlas-paper Public

    The repository with the code and analysis for the paper [Erickson et al]

    kharchenkolab/clonal-atlas-paper’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Jun 5, 2025
  • kharchenkolab/cellAdmix-Notebooks’s past year of commit activity
    Jupyter Notebook 3 MIT 0 0 0 Updated Apr 23, 2025
  • leidenAlg Public

    Implements the Leiden algorithm via an R interface

    kharchenkolab/leidenAlg’s past year of commit activity
    C 12 4 1 (1 issue needs help) 0 Updated Apr 19, 2025
  • sccore Public

    Core utilities for single-cell RNA-seq

    kharchenkolab/sccore’s past year of commit activity
    R 12 3 0 0 Updated Apr 13, 2025

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