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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 49 repositories
  • 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-2.0 246 0 2 Updated Dec 13, 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
  • isabl_cli Public

    🤖 isabl Command Line Client and SDK.

    papaemmelab/isabl_cli’s past year of commit activity
    Python 3 3 18 (1 issue needs help) 3 Updated Dec 10, 2024
  • toil_container Public

    🐳 Toil + Docker and Singularity.

    papaemmelab/toil_container’s past year of commit activity
    Python 9 MIT 6 3 0 Updated Nov 22, 2024
  • nf-purple Public

    Nextflow Pipeline to run Purple from HmfTools

    papaemmelab/nf-purple’s past year of commit activity
    Nextflow 0 0 0 1 Updated Nov 16, 2024
  • Complex_Oncoprint Public
    papaemmelab/Complex_Oncoprint’s past year of commit activity
    R 0 0 0 0 Updated Nov 8, 2024
  • ipssm-api Public

    API and CLI for IPSS-M

    papaemmelab/ipssm-api’s past year of commit activity
    HTML 0 0 1 0 Updated Nov 1, 2024
  • docker-annotsv Public

    Dockerfile for lgmgeo/AnnotSV tool

    papaemmelab/docker-annotsv’s past year of commit activity
    Dockerfile 0 0 0 0 Updated Oct 9, 2024
  • 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 May 30, 2024
  • mergeSVvcf Public Forked from ljdursi/mergevcf

    Python package and routines for merging SV VCF files

    papaemmelab/mergeSVvcf’s past year of commit activity
    Python 7 MIT 10 0 1 Updated May 23, 2024
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