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    20 repositories

    • scRNAutils

      Public
      This repo contains code for automating processing of scRNA libraries and other useful functions
      R
      •
      Other
      •3•10•3•0•Updated Sep 5, 2024Sep 5, 2024

    • PlaqView

      Public
      This is a standalone interactive Shiny tool to analyze and explore single-cell RNA-seq data from human coronary artery.
      bioinformaticsrna-seqsingle-cell
      R
      •
      Apache License 2.0
      •5•7•0•0•Updated Jul 30, 2024Jul 30, 2024

    • Dockerfile_Plaqview

      Public
      This repo contains the dockerfile(s) to accurately reproduce the environment to analyze plaqview data and develop the plaqview shiny app
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated Jan 31, 2024Jan 31, 2024

    • Human_athero_scRNA_meta

      Public
      This repo contains scripts used for the Human Atherosclerosis scRNA-seq meta-analysis project.
      Jupyter Notebook
      •2•7•3•0•Updated Oct 8, 2023Oct 8, 2023

    • toy_iSEE_instance

      Public
      This repo has code to build a small iSEE app for docker image testing purposes.
      R
      •1•0•0•0•Updated Oct 3, 2023Oct 3, 2023

    • Fine_mapping

      Public
      This repository contains scripts used for fine-mapping GWAS locus using eQTL prioritization methods, including Summary-based Mendelian Randomization (SMR) and coloc based colocalization.
      R
      •3•5•0•0•Updated Aug 16, 2023Aug 16, 2023

    • PlaqView_DataProcessing

      Public
      This is just the directory and scripts for processing the raw recruited datasets
      Jupyter Notebook
      •1•2•0•0•Updated Jul 25, 2023Jul 25, 2023

    • CAD_QTL

      Public
      R
      •
      Creative Commons Zero v1.0 Universal
      •0•2•0•0•Updated Mar 15, 2023Mar 15, 2023

    • PlaqView_ATAC

      Public
      Central Repo for the PlaqView single-cell ATAC-seq portal.
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated May 24, 2022May 24, 2022

    • Ma_2020

      Public
      Comprehensive single-cell RNA seq analysis workflow: automatic cell labeling to drug discovery and repurposing. Work from UVA CPHG Miller Lab.
      workflowseuratdrug-targeting
      R
      •1•3•0•0•Updated Apr 29, 2022Apr 29, 2022

    • Coronary_snATAC

      Public
      Jupyter Notebook
      •13•11•0•0•Updated Mar 17, 2022Mar 17, 2022

    • FHL5_Manuscript

      Public
      R
      •0•0•0•0•Updated Mar 13, 2022Mar 13, 2022

    • daviddev

      Public
      this is where david will dev plaqview_ATAC
      Dockerfile
      •0•0•0•0•Updated Dec 20, 2021Dec 20, 2021

    • shinyheatmap

      Public
      Web application for enormous biological heatmaps
      R
      •
      GNU General Public License v3.0
      •24•0•0•0•Updated Dec 8, 2021Dec 8, 2021

    • DrugThatGene

      Public
      DrugThatGene
      Python
      •5•0•0•0•Updated Oct 17, 2021Oct 17, 2021

    • LeafCutter

      Public
      UVA Miller Lab LeafCutter pipeline
      R
      •1•0•0•0•Updated Jul 20, 2021Jul 20, 2021

    • varID_rsID_converter

      Public
      varID to rsID converter
      R
      •1•0•0•0•Updated Jul 10, 2021Jul 10, 2021

    • CAD-Analysis

      Public
      0•0•0•0•Updated Mar 19, 2020Mar 19, 2020

    • Verifybam_ID

      Public
      Checks the sample contaminations and the sample swaps
      pythonrna-seqsnakemakesample-contaminationsample-swaps
      Python
      •0•0•0•0•Updated Sep 5, 2019Sep 5, 2019

    • RNA_Seq-Flow

      Public
      RNA-Seq Analysis pipeline using Snakemake workflow
      snakemakeclusterrna-seq-pipeline
      Python
      •2•1•0•0•Updated Aug 30, 2019Aug 30, 2019