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Kharchenko Lab

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  1. pagoda2 pagoda2 Public

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

    JavaScript 214 47

  2. conos conos Public

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

    R 202 39

  3. numbat numbat Public

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

    R 170 23

  4. Baysor Baysor Public

    Bayesian Segmentation of Spatial Transcriptomics Data

    Julia 158 32

  5. dropEst dropEst Public

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

    C++ 88 42

  6. scITD scITD Public

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

    R 54 2

Repositories

Showing 10 of 36 repositories
  • Baysor Public

    Bayesian Segmentation of Spatial Transcriptomics Data

    kharchenkolab/Baysor’s past year of commit activity
    Julia 158 MIT 32 16 0 Updated Dec 10, 2024
  • sccore Public

    Core utilities for single-cell RNA-seq

    kharchenkolab/sccore’s past year of commit activity
    R 12 3 0 0 Updated Dec 6, 2024
  • numbat Public

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

    kharchenkolab/numbat’s past year of commit activity
    R 170 23 68 0 Updated Dec 5, 2024
  • 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 0 0 0 0 Updated Nov 14, 2024
  • cacoa Public

    Single-cell Case Control Analysis

    kharchenkolab/cacoa’s past year of commit activity
    R 48 8 8 1 Updated Nov 5, 2024
  • leidenAlg Public

    Implements the Leiden algorithm via an R interface

    kharchenkolab/leidenAlg’s past year of commit activity
    C 9 4 1 (1 issue needs help) 0 Updated Oct 17, 2024
  • GraphPriorKMeans Public
    kharchenkolab/GraphPriorKMeans’s past year of commit activity
    Julia 0 0 0 0 Updated Oct 8, 2024
  • cellAdmix Public

    Evaluating and correcting cell admixtures in imaging-based spatial transcriptomics data

    kharchenkolab/cellAdmix’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Sep 25, 2024
  • scLiTr Public

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

    kharchenkolab/scLiTr’s past year of commit activity
    Python 3 0 0 0 Updated Aug 7, 2024
  • gpsFISH Public

    Optimization of gene panels for targeted spatial transcriptomics

    kharchenkolab/gpsFISH’s past year of commit activity
    R 7 1 3 0 Updated Jul 16, 2024
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