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@settylab

Setty Lab @ Fred Hutch

We are a multi-disciplinary research group investigation differentiation trajectories using single-cell data

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  1. Mellon Mellon Public

    Non-parametric density inference for single-cell analysis.

    Jupyter Notebook 68 4

  2. atac_metacell_utilities atac_metacell_utilities Public

    Snakemake pipeline for scATAC metacell utilities such as primed and lineage specific scores, chromVAR, in-silico ChIP

    Python 5

  3. 2for1separator 2for1separator Public

    Deconvolve CUT&Tag 2for1 data.

    Python 1

  4. Harmony Harmony Public

    Forked from dpeerlab/Harmony

    Harmony framework for connecting scRNA-seq data from discrete time points

    Jupyter Notebook

  5. Palantir Palantir Public

    Forked from dpeerlab/Palantir

    Single cell trajectory detection

    Jupyter Notebook

  6. SEACells SEACells Public

    Forked from dpeerlab/SEACells

    SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

    Jupyter Notebook 1

Repositories

Showing 10 of 26 repositories
  • kompot Public

    Differential abundance and gene expression in single-cell data

    settylab/kompot’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Apr 10, 2025
  • convert2anndata Public

    An R package to convert SingeCellExperiment and Seurat objects into anndata as comprehensively as possible.

    settylab/convert2anndata’s past year of commit activity
    R 9 GPL-3.0 2 2 0 Updated Apr 9, 2025
  • single-cell-primers Public

    Primers for single-cell data analysis

    settylab/single-cell-primers’s past year of commit activity
    Jupyter Notebook 5 MIT 2 0 1 Updated Mar 25, 2025
  • worm-glia-atlas Public

    Repository for tutorials and reproducibility notebooks for the worm glia scRNA-seq atlas

    settylab/worm-glia-atlas’s past year of commit activity
    Jupyter Notebook 0 1 0 1 Updated Mar 25, 2025
  • atac_metacell_utilities Public

    Snakemake pipeline for scATAC metacell utilities such as primed and lineage specific scores, chromVAR, in-silico ChIP

    settylab/atac_metacell_utilities’s past year of commit activity
    Python 5 0 1 3 Updated Mar 21, 2025
  • ArchR Public Forked from GreenleafLab/ArchR

    ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

    settylab/ArchR’s past year of commit activity
    R 0 MIT 145 0 0 Updated Mar 19, 2025
  • Mellon Public

    Non-parametric density inference for single-cell analysis.

    settylab/Mellon’s past year of commit activity
    Jupyter Notebook 68 GPL-3.0 4 2 0 Updated Mar 12, 2025
  • Palantir Public Forked from dpeerlab/Palantir

    Single cell trajectory detection

    settylab/Palantir’s past year of commit activity
    Jupyter Notebook 0 GPL-2.0 54 0 0 Updated Mar 3, 2025
  • mellon-feedstock Public Forked from conda-forge/mellon-feedstock

    A conda-smithy repository for mellon.

    settylab/mellon-feedstock’s past year of commit activity
    0 BSD-3-Clause 3 0 0 Updated Dec 13, 2024
  • SEACells Public Forked from dpeerlab/SEACells

    SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

    settylab/SEACells’s past year of commit activity
    Jupyter Notebook 1 GPL-2.0 30 0 0 Updated Dec 2, 2024
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