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    172 repositories

    • bfx-workshop

      Public
      A course on genomics and bioinformatics from WU
      bioinformaticsdatavizgenomicsanalysisbiologysequencingdnaalignmentrnaseqrna
      HTML
      •19•59•0•0•Updated Nov 11, 2024Nov 11, 2024

    • qc-analysis-pipeline

      Public
      Workflow used for WGS/WES data QC
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •45•8•9•0•Updated Oct 16, 2024Oct 16, 2024

    • analysis-workflows

      Public
      Open workflow definitions for genomic analysis from MGI at WUSM.
      Common Workflow Language
      •
      MIT License
      •57•102•74•15•Updated Jun 26, 2024Jun 26, 2024

    • UR

      Public
      Rich Transactional Objects for Perl
      Perl
      •
      Other
      •12•3•7•4•Updated Jun 15, 2024Jun 15, 2024

    • snvstory

      Public
      Rapid and accurate ancestry inference using SNVs.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•0•0•0•Updated May 8, 2024May 8, 2024

    • cig-pipelines

      Public
      Workflows and resources for running pipelines for somatic mutation discovery in pangenomes plus miscellaneous tools..
      WDL
      •1•0•0•0•Updated Apr 19, 2024Apr 19, 2024

    • spectacle

      Public
      Ruby
      •2•0•9•9•Updated Mar 25, 2024Mar 25, 2024

    • genome

      Public
      Core modules used by the GMS
      Perl
      •
      GNU Lesser General Public License v3.0
      •57•64•9•0•Updated Mar 13, 2024Mar 13, 2024

    • cle-myeloseqhd

      Public
      Python
      •4•2•3•0•Updated Dec 20, 2023Dec 20, 2023

    • sciclone

      Public
      An R package for inferring the subclonal architecture of tumors
      R
      •
      Other
      •55•116•4•1•Updated Oct 13, 2023Oct 13, 2023

    • scrna_mutations

      Public
      Supplementary data for Petti, et al 2019 scRNA mutation publication
      Python
      •13•16•1•0•Updated Feb 1, 2023Feb 1, 2023

    • docker-samtools-cwl

      Public
      Dockerfile
      •2•1•0•0•Updated Jan 24, 2023Jan 24, 2023

    • docker-samtools

      Public
      Docker container for Samtools
      2•0•0•0•Updated Jan 11, 2023Jan 11, 2023

    • AGFusion

      Public
      Python package to annotate and visualize gene fusions.
      Python
      •
      MIT License
      •25•4•0•0•Updated Dec 15, 2022Dec 15, 2022

    • docker-mapq0-filter

      Public
      filter a vcf for variants with high percentage of mapq0 reads
      Python
      •2•0•0•0•Updated Oct 26, 2022Oct 26, 2022

    • cle

      Public
      Repo for cle related software
      WDL
      •1•1•0•0•Updated Oct 19, 2022Oct 19, 2022

    • docker-immuno_tools-cwl

      Public
      Shell
      •0•0•7•0•Updated Aug 23, 2022Aug 23, 2022

    • bmm

      Public
      R package that uses a variational Bayesian approach to fitting a mixture of Beta distributions
      R
      •
      Other
      •9•4•2•0•Updated Aug 1, 2022Aug 1, 2022

    • docker-cnvkit

      Public
      Dockerfile
      •3•0•0•0•Updated May 25, 2022May 25, 2022

    • docker-fastqc-cwl

      Public
      Dockerfile
      •0•0•0•0•Updated May 25, 2022May 25, 2022

    • fpfilter-tool

      Public
      Perl
      •21•6•0•1•Updated Apr 27, 2022Apr 27, 2022

    • docker-vep_helper-cwl

      Public
      Perl
      •3•0•1•0•Updated Apr 5, 2022Apr 5, 2022

    • docker-somatic-llr-filter

      Public
      Container for the somatic-llr filter
      Python
      •2•0•0•0•Updated Mar 11, 2022Mar 11, 2022

    • hic-pipeline

      Public
      HiC uniform processing pipeline
      WDL
      •
      MIT License
      •24•0•0•0•Updated Feb 4, 2022Feb 4, 2022

    • bam-readcount

      Public
      Count bases in BAM/CRAM files
      CMake
      •
      MIT License
      •95•305•51•0•Updated Jan 31, 2022Jan 31, 2022

    • qc-metric-aggregator

      Public
      Given the output directory of a QC pipeline and a threshold config file, parse out the desired metrics and evalute them against the thresholds.
      Python
      •
      MIT License
      •2•1•5•0•Updated Nov 4, 2021Nov 4, 2021

    • cle-myeloseq

      Public
      Repo for cle myeloseq/haloplex assay
      Perl
      •1•1•0•0•Updated Oct 8, 2021Oct 8, 2021

    • docker-bam-readcount

      Public
      Docker containerization for "bam-readcount"
      Dockerfile
      •4•0•0•1•Updated Oct 8, 2021Oct 8, 2021

    • docker-bam_readcount_helper-cwl

      Public
      Python
      •9•3•2•1•Updated Jul 8, 2021Jul 8, 2021

    • docker-homer

      Public
      fork of the quay.io homer image, moving annotations to my hardcoded link
      Dockerfile
      •4•0•0•0•Updated Jun 11, 2021Jun 11, 2021