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    28 repositories

    • astyanax-adult-brain-atlas

      Public
      Scripts and notebooks for Astyanax adult brain atlas
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jun 16, 2026Jun 16, 2026

    • 6dpf_brains

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • hic-scaffolding-nf

      Public
      Nextflow pipeline for scaffolding genome assemblies with Hi-C reads
      Nextflow
      •
      MIT License
      •5•16•2•0•Updated Nov 5, 2025Nov 5, 2025

    • agptools

      Public
      Tools for working with agp files
      Python
      •
      MIT License
      •3•19•1•0•Updated Jun 26, 2025Jun 26, 2025

    • minigraph-cactus-nf

      Public
      a nextflow pipeline for creating a pangenome with minigraph-cactus
      Nextflow
      •
      GNU General Public License v3.0
      •4•16•1•0•Updated Sep 13, 2024Sep 13, 2024

    • cleanup-ncbi-gtf

      Public
      Clean up NCBI gtf to make them compatible with cellranger
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 13, 2024Mar 13, 2024

    • chicken-pangenome-paper

      Public
      Scripts used to perform analyses in Rice et al. (2023)
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•16•0•0•Updated Dec 28, 2023Dec 28, 2023

    • giraffe-svs-nf

      Public
      Genotyping structural variants with pangenomes
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 1, 2023Dec 1, 2023

    • permute-vcf

      Public
      randomly permute the locations of variants in a vcf
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 31, 2023Oct 31, 2023

    • scanpy

      Public
      Single-Cell Analysis in Python. Scales to >1M cells.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •770•1•0•0•Updated Oct 4, 2023Oct 4, 2023

    • giraffe-slurm

      Public
      scripts to run giraffe and related pre- and post-processing on slurm
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 24, 2023Apr 24, 2023

    • giraffe-nf

      Public
      Nextflow pipeline for running vg giraffe
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 5, 2023Apr 5, 2023

    • pyslingshot

      Public
      Python implementation of the Slingshot pseudotime algorithm
      Jupyter Notebook
      •10•1•0•0•Updated Mar 14, 2023Mar 14, 2023

    • mask-repeats-nf

      Public
      simple RepeatModeler/Masker pipeline
      Nextflow
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 13, 2023Mar 13, 2023

    • cellranger-nf

      Public
      nextflow pipeline for running cellranger
      Nextflow
      •
      GNU General Public License v3.0
      •1•1•2•0•Updated Mar 13, 2023Mar 13, 2023

    • docs

      Public
      docs for various Warren Lab stuff
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Mar 8, 2023Mar 8, 2023

    • shortread-polish-nf

      Public
      Nextflow pipeline for polishing an assembly with short reads and freebayes
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 26, 2022Jul 26, 2022

    • single-cell

      Public
      Pipelines and scripts for single-cell best practices
      R
      •
      MIT License
      •2•7•0•0•Updated Jun 1, 2022Jun 1, 2022

    • longread-svs-nf

      Public
      nextflow pipeline for finding structural variants using long reads
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 21, 2022Feb 21, 2022

    • gtfez

      Public
      Really simple utilities for reading and writing gtf files
      Python
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Feb 2, 2022Feb 2, 2022

    • gffutils

      Public
      GFF and GTF file manipulation and interconversion
      Python
      •
      MIT License
      •81•0•0•0•Updated Oct 1, 2021Oct 1, 2021

    • purge-haplotigs-nf

      Public
      Nextflow workflow for purging haplotigs from a genome assembly
      Nextflow
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated Sep 24, 2021Sep 24, 2021

    • longread-polish-nf

      Public
      Nextflow pipeline for polishing an assembly with long reads and racon
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 29, 2021Jul 29, 2021

    • sra_downloader

      Public
      Easily download fastqs from SRA
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 14, 2021Jun 14, 2021

    • single-cell-ircf

      Public
      Single cell scripts from MU's IRCF
      Python
      •1•0•3•0•Updated Feb 20, 2021Feb 20, 2021

    • batch_GATK_workflow

      Public
      Batch script for running entire GATK workflow
      Shell
      •2•1•0•0•Updated Oct 7, 2020Oct 7, 2020

    • wiki

      Public
      Our lab wiki
      0•0•0•0•Updated Jun 2, 2020Jun 2, 2020

    • helen

      Public
      H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
      Python
      •
      MIT License
      •12•0•0•0•Updated May 16, 2020May 16, 2020
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