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Kharchenko Lab

Popular repositories

  1. pagoda2 pagoda2 Public

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

    JavaScript 193 46

  2. conos conos Public

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

    R 189 38

  3. numbat numbat Public

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

    R 157 22

  4. Baysor Baysor Public

    Bayesian Segmentation of Spatial Transcriptomics Data

    Julia 139 27

  5. dropEst dropEst Public

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

    C++ 84 43

  6. cacoa cacoa Public

    Single-cell Case Control Analysis

    R 44 7

Repositories

Showing 10 of 34 repositories
  • scLiTr Public

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

    Python 0 0 0 0 Updated Jun 7, 2024
  • clonal-atlas-paper Public

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

    Jupyter Notebook 0 0 0 0 Updated Jun 7, 2024
  • numbat Public

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

    R 157 22 61 0 Updated Jun 4, 2024
  • Baysor Public

    Bayesian Segmentation of Spatial Transcriptomics Data

    Julia 139 MIT 27 32 1 Updated Jun 4, 2024
  • thymus-mesenchyme Public

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

    Jupyter Notebook 0 0 0 0 Updated Jun 2, 2024
  • scITD Public

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

    R 34 0 4 0 Updated Apr 14, 2024
  • hahmmr Public

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

    R 13 0 1 0 Updated Apr 2, 2024
  • cacoa Public

    Single-cell Case Control Analysis

    R 44 7 9 1 Updated Mar 8, 2024
  • leidenAlg Public

    Implements the Leiden algorithm via an R interface

    C 9 4 1 (1 issue needs help) 0 Updated Feb 27, 2024
  • pagoda2 Public

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

    JavaScript 193 46 0 0 Updated Feb 27, 2024
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