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WarrenLab

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  1. chicken-pangenome-paper chicken-pangenome-paper Public

    Scripts used to perform analyses in Rice et al. (2023)

    Jupyter Notebook 15 2

  2. hic-scaffolding-nf hic-scaffolding-nf Public

    Nextflow pipeline for scaffolding genome assemblies with Hi-C reads

    Nextflow 14 4

  3. minigraph-cactus-nf minigraph-cactus-nf Public

    a nextflow pipeline for creating a pangenome with minigraph-cactus

    Nextflow 14 4

  4. agptools agptools Public

    Tools for working with agp files

    Python 8 2

  5. single-cell single-cell Public

    Pipelines and scripts for single-cell best practices

    R 7 2

  6. purge-haplotigs-nf purge-haplotigs-nf Public

    Nextflow workflow for purging haplotigs from a genome assembly

    Nextflow 3

Repositories

Showing 10 of 26 repositories
  • hic-scaffolding-nf Public

    Nextflow pipeline for scaffolding genome assemblies with Hi-C reads

    WarrenLab/hic-scaffolding-nf’s past year of commit activity
    Nextflow 14 MIT 4 3 0 Updated Dec 20, 2024
  • minigraph-cactus-nf Public

    a nextflow pipeline for creating a pangenome with minigraph-cactus

    WarrenLab/minigraph-cactus-nf’s past year of commit activity
    Nextflow 14 GPL-3.0 4 1 0 Updated Sep 13, 2024
  • cleanup-ncbi-gtf Public

    Clean up NCBI gtf to make them compatible with cellranger

    WarrenLab/cleanup-ncbi-gtf’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Mar 13, 2024
  • agptools Public

    Tools for working with agp files

    WarrenLab/agptools’s past year of commit activity
    Python 8 MIT 2 1 0 Updated Mar 6, 2024
  • chicken-pangenome-paper Public

    Scripts used to perform analyses in Rice et al. (2023)

    WarrenLab/chicken-pangenome-paper’s past year of commit activity
    Jupyter Notebook 15 GPL-3.0 2 0 0 Updated Dec 28, 2023
  • giraffe-svs-nf Public

    Genotyping structural variants with pangenomes

    WarrenLab/giraffe-svs-nf’s past year of commit activity
    Nextflow 0 GPL-3.0 0 0 0 Updated Dec 1, 2023
  • permute-vcf Public

    randomly permute the locations of variants in a vcf

    WarrenLab/permute-vcf’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Oct 31, 2023
  • scanpy Public Forked from scverse/scanpy

    Single-Cell Analysis in Python. Scales to >1M cells.

    WarrenLab/scanpy’s past year of commit activity
    Python 1 BSD-3-Clause 613 0 0 Updated Oct 4, 2023
  • giraffe-slurm Public

    scripts to run giraffe and related pre- and post-processing on slurm

    WarrenLab/giraffe-slurm’s past year of commit activity
    Shell 0 GPL-3.0 0 0 0 Updated Apr 24, 2023
  • giraffe-nf Public

    Nextflow pipeline for running vg giraffe

    WarrenLab/giraffe-nf’s past year of commit activity
    0 GPL-3.0 0 0 0 Updated Apr 5, 2023
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