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    42 repositories

    • CUT-Tag-workflow

      Public
      This workflow performs trimming, alignment, and generates BigWig and BED files for CUT&Tag data. The workflow is optimized for the HPC environment at Van Andel Institute, but it can be easily modified for general use on other systems.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 24, 2025Dec 24, 2025

    • prep_bbc_shared

      Public
      Pipeline for preparing shared resources such as aligner index files in the BBC.
      Python
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Dec 19, 2025Dec 19, 2025

    • rnaseq_workflow

      Public
      snakemake workflow for bulk RNA-seq workflow using STAR-edgeR
      snakemakepipelinernaseq
      Python
      •
      GNU General Public License v3.0
      •17•13•1•0•Updated Dec 2, 2025Dec 2, 2025

    • Social_distancing_and_activity_analysis

      Public
      R code to analyze social distancing and activity analyses of drosophila. Current implementation utilizes control mutants to establish null intervals for use with a second generation p-values. Activity data are analyzed using PC regression.
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 13, 2025Nov 13, 2025

    • demultiplex

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Nov 3, 2025Nov 3, 2025

    • Nauta_2025

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 28, 2025Oct 28, 2025

    • snakemake_template

      Public template
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 28, 2025Oct 28, 2025

    • bioinfo_workshop_2025

      Public
      Jupyter Notebook
      •0•3•0•0•Updated Oct 23, 2025Oct 23, 2025

    • nextflow_template

      Public template
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • Intro_to_Linux_for_HPC

      Public
      Euphoria
      •3•0•0•0•Updated Oct 3, 2025Oct 3, 2025

    • insitu_probe_generator

      Public
      Fork of https://github.com/rwnull/insitu_probe_generator.git v.0.3.2
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Sep 16, 2025Sep 16, 2025

    • Mouse-to-Usable_M2U

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • EVITA_Analysis

      Public
      Analysis code pertaining to the EVI-2 manuscript titled "Oral vitamin C supplementation in patients with low-risk myeloid malignances and clonal cytopenia of undetermined significance: Results from EVI-2, a randomized, placebo-controlled phase 2 study "
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 25, 2025Jul 25, 2025

    • VAI-BBC-genomics-randomization-pipeline

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 6, 2025May 6, 2025

    • LineageSwitch_Eiken_VBCS-1416

      Public
      A spot to share our code for the lineage switch meta analysis project!
      HTML
      •0•1•0•0•Updated Apr 17, 2025Apr 17, 2025

    • VBCS-1355

      Public
      HTML
      •0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • methylation_array

      Public
      R
      •0•0•2•0•Updated Apr 7, 2025Apr 7, 2025

    • gradient-metabolomics-VBCS-1384

      Public
      A shareable code space between Hannah Damico (VAI BBC) + Richard Cassidy (VAI Fondufe-Mittendorf Lab)
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

    • Ugcg-KO_proteomics_analysis

      Public
      Proteomics + Enrichment analysis code for comparing Ugcg-KO samples
      Other
      •0•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • BBC-Workflows-CurrentPackages

      Public
      Creating a repo to save functions that we've made + currently packages or functions that we prefer for certain methods.
      Other
      •0•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • VAI-RWorkshop-2024

      Public
      Accessing documents from VAI R workshop 2024
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • Peaks_workflow

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•2•0•Updated Oct 22, 2024Oct 22, 2024

    • Fly_Analysis

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • KOBOLD_Scripts

      Public
      Proteomics analysis scripts for KOBOLD including GSEAs
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 20, 2024Jun 20, 2024

    • scRNAseq

      Public
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated May 11, 2024May 11, 2024

    • rnaseq_w_umis

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 22, 2024Apr 22, 2024

    • RCR_central_tenets

      Public
      This repo was built to house all materials for the RCR course on statistics. Slides: https://www.menti.com/aldbupw35t27. Shiny link: https://vai-bbc.shinyapps.io/RCR_Slides_20240417/
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 17, 2024Apr 17, 2024

    • Drosophilia_Single_Embryo_Workflow

      Public
      Workflow accompanying manuscript titled: Single-embryo metabolomics reveals developmental metabolism in the early Drosophila embryo
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 3, 2024Apr 3, 2024

    • Biscuit_Snakemake_Workflow

      Public archive
      Snakemake Workflow For WGBS Data
      Python
      •
      GNU General Public License v3.0
      •12•3•0•0•Updated Nov 30, 2023Nov 30, 2023

    • variants-gatk4

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Oct 27, 2023Oct 27, 2023