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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 66 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 25 repositories
  • Palantir Public Forked from dpeerlab/Palantir

    Single cell trajectory detection

    settylab/Palantir’s past year of commit activity
    Jupyter Notebook 0 GPL-2.0 55 0 0 Updated Mar 3, 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 8 GPL-3.0 2 2 0 Updated Feb 26, 2025
  • Mellon Public

    Non-parametric density inference for single-cell analysis.

    settylab/Mellon’s past year of commit activity
    Jupyter Notebook 66 GPL-3.0 4 4 0 Updated Feb 13, 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
  • 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 Dec 6, 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 28 0 0 Updated Dec 2, 2024
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Conda recipes for the bioconda channel.

    settylab/bioconda-recipes’s past year of commit activity
    Shell 0 MIT 3,406 0 0 Updated Nov 30, 2024
  • proseg-workflow Public

    Proseg nextflow pipeline for Cirro

    settylab/proseg-workflow’s past year of commit activity
    Nextflow 1 0 3 0 Updated Nov 6, 2024
  • 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 0 Updated Jul 24, 2024
  • kdpeak Public

    A kernel density estimation based peak caller

    settylab/kdpeak’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Jul 23, 2024
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