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  1. pagoda2 pagoda2 Public

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

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  2. conos conos Public

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

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

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

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  • Jupyter Notebook 1 MIT 0 0 0 Updated Apr 23, 2025
  • cellAdmix Public
    Jupyter Notebook 1 MIT 0 0 0 Updated Apr 23, 2025
  • leidenAlg Public

    Implements the Leiden algorithm via an R interface

    C 9 4 1 (1 issue needs help) 0 Updated Apr 19, 2025
  • sccore Public

    Core utilities for single-cell RNA-seq

    R 12 3 0 0 Updated Apr 13, 2025
  • numbat Public

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

    R 181 24 76 0 Updated Mar 19, 2025
  • Baysor Public

    Bayesian Segmentation of Spatial Transcriptomics Data

    Julia 170 MIT 34 26 0 Updated Dec 10, 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 Nov 14, 2024
  • cacoa Public

    Single-cell Case Control Analysis

    R 48 10 9 1 Updated Nov 5, 2024
  • Julia 0 0 0 0 Updated Oct 8, 2024
  • cellAdmix-preprint Public

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

    Jupyter Notebook 0 1 1 0 Updated Sep 25, 2024

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