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@papaemmelab

Elli Papaemmanuil Lab

We study the role of acquired mutations in cancer development and how these determine clinical phenotype and response to therapy.

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  1. ipssm ipssm Public

    Molecular International Prognostic Scoring System IPSS-M for Myelodysplastic Syndromes

    R 8 5

  2. toil_container toil_container Public

    🐳 Toil + Docker and Singularity.

    Python 9 6

  3. split_bed_by_index split_bed_by_index Public

    Split bed intervals by estimated read counts from bam index

    Nim 9

  4. split_bed_by_reads split_bed_by_reads Public

    Split bed intervals by maximum read counts

    Nim 9

  5. cookiecutter-toil cookiecutter-toil Public

    🍪 Cookiecutter template for Class Based Toil pipelines.

    Python 4 1

  6. register_apps register_apps Public

    👾 Register versioned toil container pipelines in a bin directory as singularity images.

    Python 6

Repositories

Showing 10 of 52 repositories
  • Complex_Oncoprint Public
    papaemmelab/Complex_Oncoprint’s past year of commit activity
    R 0 0 0 0 Updated Apr 3, 2025
  • nf-core-modules Public Forked from nf-core/modules

    Repository to host tool-specific module files for the Nextflow DSL2 community!

    papaemmelab/nf-core-modules’s past year of commit activity
    Nextflow 0 MIT 838 0 0 Updated Apr 1, 2025
  • nf-core-test-datasets-fork Public Forked from nf-core/test-datasets

    Test data to be used for automated testing with the nf-core pipelines

    papaemmelab/nf-core-test-datasets-fork’s past year of commit activity
    0 MIT 391 0 0 Updated Mar 26, 2025
  • nf-proteinactivity Public

    nf-core modules to compute protein activity network interactions

    papaemmelab/nf-proteinactivity’s past year of commit activity
    Nextflow 0 0 0 0 Updated Mar 25, 2025
  • isabl_cli Public

    🤖 isabl Command Line Client and SDK.

    papaemmelab/isabl_cli’s past year of commit activity
    Python 4 4 19 (2 issues need help) 3 Updated Mar 5, 2025
  • ipssm-api Public

    API and CLI for IPSS-M

    papaemmelab/ipssm-api’s past year of commit activity
    HTML 0 0 1 0 Updated Feb 19, 2025
  • toil Public Forked from DataBiosphere/toil

    A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

    papaemmelab/toil’s past year of commit activity
    Python 0 Apache-2.0 247 0 2 Updated Feb 12, 2025
  • nf-purple Public

    Nextflow Pipeline to run Purple from HmfTools

    papaemmelab/nf-purple’s past year of commit activity
    Nextflow 0 0 0 0 Updated Jan 7, 2025
  • register_apps Public

    👾 Register versioned toil container pipelines in a bin directory as singularity images.

    papaemmelab/register_apps’s past year of commit activity
    Python 6 MIT 0 1 1 Updated Dec 28, 2024
  • CaVEMan Public Forked from cancerit/CaVEMan

    SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

    papaemmelab/CaVEMan’s past year of commit activity
    C 0 AGPL-3.0 16 0 0 Updated Dec 10, 2024
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