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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 202 47

  2. conos conos Public

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

    R 191 38

  3. numbat numbat Public

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

    R 161 23

  4. Baysor Baysor Public

    Bayesian Segmentation of Spatial Transcriptomics Data

    Julia 144 29

  5. dropEst dropEst Public

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

    C++ 85 43

  6. cacoa cacoa Public

    Single-cell Case Control Analysis

    R 46 7

Repositories

Showing 10 of 35 repositories
  • scLiTr Public

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

    kharchenkolab/scLiTr’s past year of commit activity
    Python 2 0 0 0 Updated Aug 7, 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 Aug 7, 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 Jul 30, 2024
  • gpsFISH Public

    Optimization of gene panels for targeted spatial transcriptomics

    kharchenkolab/gpsFISH’s past year of commit activity
    R 6 1 2 0 Updated Jul 16, 2024
  • Baysor Public

    Bayesian Segmentation of Spatial Transcriptomics Data

    kharchenkolab/Baysor’s past year of commit activity
    Julia 144 MIT 29 34 0 Updated Jun 18, 2024
  • numbat Public

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

    kharchenkolab/numbat’s past year of commit activity
    R 161 23 65 0 Updated Jun 4, 2024
  • 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 0 0 0 0 Updated Jun 2, 2024
  • scITD Public

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

    kharchenkolab/scITD’s past year of commit activity
    R 34 0 4 0 Updated Apr 14, 2024
  • hahmmr Public

    Haplotype-aware Hidden Markov Models for detecting CNVs from bulk RNA-seq

    kharchenkolab/hahmmr’s past year of commit activity
    R 13 0 1 0 Updated Apr 2, 2024
  • cacoa Public

    Single-cell Case Control Analysis

    kharchenkolab/cacoa’s past year of commit activity
    R 46 7 9 1 Updated Mar 8, 2024
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