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@powellgenomicslab Single Cell Computational Genomics

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    47 repositories

    • AMD_RPD

      Public
      AMD: RPD vs drusen
      R
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • NCI_SNP_imputation_1000g_hg38

      Public
      pipeline for imputing snps on 1000g hg38 reference. repurposed from sceQTL-Gen for specific lab use
      Python
      •1•0•0•0•Updated Apr 15, 2026Apr 15, 2026

    • tenk10k_phase1_multiome

      Public
      The computational and statistical analyses of TenK10K phase 1 multiome data
      Jupyter Notebook
      •
      MIT License
      •0•13•0•0•Updated Apr 7, 2026Apr 7, 2026

    • tensorqtl-ase

      Public
      Ultrafast GPU-enabled QTL mapper with gpu accelerated re-implementations of MixQTL and Combined Haplotype Test
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •63•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • sc-veQTL

      Public
      Analysis code for sc-veQTL study
      R
      •
      GNU General Public License v3.0
      •1•9•0•0•Updated Mar 8, 2026Mar 8, 2026

    • tenk10k_phase1

      Public
      Repo for analyses of the pilot phase of TenK10K
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Mar 2, 2026Mar 2, 2026

    • scDeepID_TenK10K_manuscripts

      Public
      source code of scDeepID used in TenK10K manuscripts
      Python
      •0•0•0•0•Updated Feb 27, 2026Feb 27, 2026

    • ILD-BAL-scRNA-Manuscript-2025

      Public
      This repository contains the code used to analyze single-cell RNA data from bronchoalveolar lavage fluid from interstitial lung disease patient samples. In subm…
      Jupyter Notebook
      •0•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • Nebulosa

      Public
      R package to visualize gene expression data based on weighted kernel density estimation
      single-cellsingle-cell-rna-seqsingle-cell-analysis
      single-cellsingle-cell-rna-seqsingle-cell-analysissingle-cell-multiomics
      R
      •16•112•27•3•Updated Feb 6, 2026Feb 6, 2026

    • tenk10k_cohort_specific_eQTL

      Public
      This repo contains the scripts for a summer project led by Jonathan Johnson, which aims to compare the eQTL difference between the TOB and BioHeart cohorts.
      Python
      •0•1•0•0•Updated Feb 6, 2026Feb 6, 2026

    • PEER_factors

      Public
      Contains analysis code to generate PEER factors from pseudo-bulk data and perform eQTL association analysis
      R
      •
      GNU General Public License v3.0
      •1•7•1•0•Updated Feb 3, 2026Feb 3, 2026

    • nci-job-parser

      Public
      Utility program to parse NCI job output
      Python
      •
      MIT License
      •1•0•0•0•Updated Oct 30, 2025Oct 30, 2025

    • tenk10k-causal-paper

      Public
      TenK10K causal inference manuscript
      R
      •
      MIT License
      •0•7•0•0•Updated Sep 10, 2025Sep 10, 2025

    • SingularityBaseImages

      Public
      Singularity base images that will be build on singularity hub and can be used to build other images
      0•1•0•0•Updated Jul 13, 2025Jul 13, 2025

    • LBIOtoxicity

      Public
      Jen's PhD LBIO pilot coding
      R
      •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

    • Demuxafy_manuscript

      Public
      Scripts used for manuscript for Demuxafy
      R
      •
      MIT License
      •0•0•0•0•Updated Mar 13, 2024Mar 13, 2024

    • scPred

      Public
      scPred package for cell type prediction from scRNA-seq data
      R
      •
      MIT License
      •20•100•22•1•Updated Jan 18, 2024Jan 18, 2024

    • Utilities

      Public
      A compilation of useful snippets for use on Brenner.
      Python
      •0•0•0•0•Updated Aug 9, 2023Aug 9, 2023

    • hypothalamus_organoid_scRNA

      Public
      Code used to analyze hypothalamus organoid single cell RN
      R
      •0•0•0•0•Updated Jul 10, 2023Jul 10, 2023

    • iPSC_Village_scripts

      Public
      scripts used to analyze the iPSC village project
      R
      •0•1•0•0•Updated May 6, 2023May 6, 2023

    • Powell_lab_resources

      Public
      A public GitHub repo to share resources for common computational challenges
      MIT License
      •0•1•0•0•Updated Apr 28, 2023Apr 28, 2023

    • SNP_imputation_1000g_hg38

      Public
      pipeline for imputing snps on 1000g hg38 reference. repurposed from sceQTL-Gen for specific lab use
      Python
      •1•1•0•0•Updated Feb 6, 2023Feb 6, 2023

    • WG2-pipeline-classification-docs

      Public
      WG2 documentation website for cell type classification
      HTML
      •2•0•0•0•Updated Feb 3, 2023Feb 3, 2023

    • iPSC_Village_Publication

      Public
      R
      •0•0•0•0•Updated Jan 28, 2023Jan 28, 2023

    • OneK1K-Web-browser

      Public
      HTML
      •2•1•0•56•Updated Jan 6, 2023Jan 6, 2023

    • ancestry_prediction_scRNAseq

      Public
      Use SNP genotype information pulled from single cell RNA-seq data to predict ancestries
      Python
      •0•0•0•0•Updated Nov 22, 2022Nov 22, 2022

    • Imputation_pipeline

      Public
      Imputation workflow with sanger impuation server, originally prepared for sceQTL-Gen consortium but copied here on 30 August, 2021 when updating to hg38 for sce…
      Python
      •0•0•0•0•Updated Mar 31, 2022Mar 31, 2022

    • onek1k_scd

      Public
      Phase 2 analysis for OneK1K data in hg38 and new cell type annotation
      R
      •1•2•0•0•Updated Feb 22, 2022Feb 22, 2022

    • CellRankJupyter

      Public
      Dockerfile for Cell Rank Jupyter notebooks - includes scanpy, velocyto, scvelo and CellRank
      Dockerfile
      •0•2•0•0•Updated Jan 24, 2022Jan 24, 2022

    • Braque

      Public
      Braque provides a collection of methods to perform pseudo-bulk analysis from single-cell data.
      R
      •
      Other
      •0•1•0•0•Updated Dec 9, 2021Dec 9, 2021
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