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@powellgenomicslab Single Cell Computational Genomics

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    36 repositories

    • 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•5•0•0•Updated Oct 3, 2024Oct 3, 2024

    • sc-veQTL

      Public
      Analysis code for sc-veQTL study
      R
      •
      GNU General Public License v3.0
      •1•6•0•0•Updated Jun 24, 2024Jun 24, 2024

    • Demuxafy_manuscript

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

    • Nebulosa

      Public
      R package to visualize gene expression data based on weighted kernel density estimation
      single-cellsingle-cell-rna-seqsingle-cell-analysissingle-cell-multiomics
      R
      •8•91•23•1•Updated Feb 27, 2024Feb 27, 2024

    • scPred

      Public
      scPred package for cell type prediction from scRNA-seq data
      R
      •
      MIT License
      •16•79•20•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
      •0•0•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 sceQTL-Gen consortium
      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
      •0•0•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

    • DropletQC_paper

      Public
      Analysis code and figures for the DropletQC manuscript
      R
      •0•2•0•0•Updated Nov 18, 2021Nov 18, 2021

    • DropletQC

      Public
      Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data
      scrna-seqempty-dropletsqc-metricambient-rna
      R
      •
      Other
      •3•34•5•0•Updated Nov 18, 2021Nov 18, 2021

    • onek1k_dea

      Public
      Characterization of transcriptional heterogeneity in OneK1K project
      R
      •0•2•0•0•Updated Nov 10, 2021Nov 10, 2021

    • onek1k_phase1

      Public
      Contains code to analyze the OneK1K data and perform eQTL mapping of 14 cell types
      R
      •7•24•3•0•Updated Oct 13, 2021Oct 13, 2021

    • BGI_vs_Illumina_Benchmark

      Public
      This repository contains code related to the publication "Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing" by Senabouth et al.
      Shell
      •8•15•1•0•Updated Oct 12, 2021Oct 12, 2021

    • WG1-pipeline-QC

      Public
      Part of the sc-eQTLgen consortium pipeline. Step 1, where the QC is done.
      Python
      •6•0•0•0•Updated Jun 15, 2021Jun 15, 2021

    • gatk4-rnaseq-germline-snps-indels

      Public
      Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •38•0•0•0•Updated May 10, 2021May 10, 2021

    • fusion_twas

      Public
      methods for functional summary-based imputation
      R
      •
      GNU General Public License v3.0
      •45•0•0•0•Updated May 3, 2021May 3, 2021

    • 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 Nov 24, 2020Nov 24, 2020

    • QTL_to_PredictDB

      Public
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Nov 18, 2020Nov 18, 2020

    • CROP-seq

      Public
      Repository for the processing and analysis of CROP-seq data
      R
      •5•6•0•2•Updated Nov 17, 2020Nov 17, 2020

    • plasmablasts_and_neutrophils

      Public
      HTML
      •0•0•0•0•Updated Oct 1, 2020Oct 1, 2020