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    19 repositories

    • seqslab-api-reference

      Public
      SeqsLab REST API YAML files for docs.atgenomix.com
      0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • seqslab-operators

      Public
      Atgenomix Operators are SeqsLab platform plugins and open-source Cromwell extensions that streamline heterogeneous data integration and transformation, and scale complex workflow tasks, using distributed computing clusters and GPU accelerators.
      Scala
      •
      Apache License 2.0
      •0•0•1•1•Updated Oct 18, 2024Oct 18, 2024

    • shinyapps

      Public
      Shiny apps on Atgenomix SeqsLab
      R
      •
      Apache License 2.0
      •0•0•2•1•Updated Oct 14, 2024Oct 14, 2024

    • sparklyr

      Public
      R interface for Apache Spark
      R
      •
      Apache License 2.0
      •310•0•0•0•Updated Sep 22, 2024Sep 22, 2024

    • support

      Public
      0•0•0•0•Updated Sep 22, 2024Sep 22, 2024

    • superset

      Public
      Apache Superset is a Data Visualization and Data Exploration Platform
      TypeScript
      •
      Apache License 2.0
      •14k•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • seqslab-connector

      Public
      SeqsLab cluster and data lakehouse connector for Python
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Jul 10, 2024Jul 10, 2024

    • spark-operator

      Public
      Kubernetes operator for managing the lifecycle of Apache Spark applications on Kubernetes.
      Go
      •
      Apache License 2.0
      •1.4k•0•0•0•Updated Jun 2, 2024Jun 2, 2024

    • assets

      Public
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Apr 10, 2024Apr 10, 2024

    • sample-sheet

      Public
      Parse Illumina sample sheets with Python
      Python
      •
      MIT License
      •16•0•0•0•Updated Dec 18, 2023Dec 18, 2023

    • connectedreads

      Public
      a machine-learning optimized long-range genome analysis workflow for next-generation sequencing
      Scala
      •
      Apache License 2.0
      •0•1•0•2•Updated Sep 29, 2023Sep 29, 2023

    • JSON-schemas

      Public
      JSON schemas for genomics and health data exchange and forms
      Apache License 2.0
      •0•0•1•1•Updated Jul 26, 2023Jul 26, 2023

    • seqslab-docs-operator-pipeline-api

      Public
      API docs for SeqsLab operator pipeline in distributed workflow execution
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 8, 2023Mar 8, 2023

    • deepvariant-on-spark

      Public
      DeepVariant-on-Spark is a germline short variant calling pipeline that runs Google DeepVariant on Apache Spark at scale.
      bioinformaticsgenomicsngssequencingdnadeep-neural-networkdeepvariantsparkadam
      Shell
      •
      Apache License 2.0
      •5•13•3•0•Updated May 4, 2022May 4, 2022

    • hail

      Public
      Scalable genomic data analysis.
      Scala
      •
      MIT License
      •247•1•0•0•Updated Feb 21, 2021Feb 21, 2021

    • workflow-execution-service-schemas

      Public
      The WES API is a standard way to run and manage portable workflows.
      Python
      •
      Apache License 2.0
      •38•0•0•0•Updated Oct 10, 2020Oct 10, 2020

    • cromwell

      Public archive
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •359•0•0•0•Updated Sep 16, 2020Sep 16, 2020

    • deepvariant

      Public
      DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •728•1•0•0•Updated Jul 11, 2019Jul 11, 2019

    • graphseq

      Public
      String Graph Construction on Spark
      bioinformaticsgenomicsdenovo-assemblystring-graphspark
      Python
      •0•3•0•0•Updated May 15, 2018May 15, 2018