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    • isabl_cli

      Public
      🤖 isabl Command Line Client and SDK.
      Python
      Other
      33162Updated Oct 21, 2024Oct 21, 2024
    • Dockerfile for lgmgeo/AnnotSV tool
      Dockerfile
      0000Updated Oct 9, 2024Oct 9, 2024
    • R
      0000Updated Oct 4, 2024Oct 4, 2024
    • ipssm-api

      Public
      API and CLI for IPSS-M
      HTML
      MIT License
      0013Updated Oct 1, 2024Oct 1, 2024
    • nf-purple

      Public
      Nextflow Pipeline to run Purple from HmfTools
      Nextflow
      0001Updated Aug 14, 2024Aug 14, 2024
    • toil

      Public
      A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
      Python
      Apache License 2.0
      241002Updated Aug 2, 2024Aug 2, 2024
    • 👾 Register versioned toil container pipelines in a bin directory as singularity images.
      Python
      MIT License
      0611Updated May 30, 2024May 30, 2024
    • Python package and routines for merging SV VCF files
      Python
      MIT License
      10701Updated May 23, 2024May 23, 2024
    • 🐳 Toil + Docker and Singularity.
      Python
      MIT License
      6920Updated May 21, 2024May 21, 2024
    • hileup

      Public
      horizontal pileup
      C
      Apache License 2.0
      3000Updated Jan 16, 2024Jan 16, 2024
    • ICBBB 2023: Predicting Single Cell Genotypes from Single Cell Expression Profiles in AML Using Deep Learning
      Python
      0000Updated Nov 21, 2023Nov 21, 2023
    • 🐳 Docker container with several HMF tools installed
      Dockerfile
      0000Updated Sep 5, 2023Sep 5, 2023
    • Gao_NC_CH

      Public
      Code and Data for Gao et al., Nature Communications 2021
      Jupyter Notebook
      2600Updated Aug 16, 2023Aug 16, 2023
    • Code accompanying "High-Resolution Interpretable Classification of Artifacts versus Real Variants in Whole Genome Sequencing Data from Archived Tissue" by Domenico & Asimomitis et al. https://icml-compbio.github.io/2023/papers/WCBICML2023_paper116.pdf
      Jupyter Notebook
      1100Updated Aug 9, 2023Aug 9, 2023
    • papaemmelab

      Public template
      👩🏻‍🔬 The Papaemmanuil Lab Website
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      310000Updated Aug 7, 2023Aug 7, 2023
    • toil_hla

      Public
      🧬 Toil workflow for HLA typing tools.
      Python
      MIT License
      0000Updated May 23, 2023May 23, 2023
    • IPSS-M study
      HTML
      01000Updated Apr 3, 2023Apr 3, 2023
    • Data for Shukla, Levine, Gundem et al.
      Jupyter Notebook
      1500Updated Apr 3, 2023Apr 3, 2023
    • R
      0000Updated Mar 29, 2023Mar 29, 2023
    • cnvkit

      Public
      Copy number variant detection from targeted DNA sequencing
      Python
      Other
      165000Updated Mar 16, 2023Mar 16, 2023
    • ipssm

      Public
      Molecular International Prognostic Scoring System IPSS-M for Myelodysplastic Syndromes
      R
      Other
      5810Updated Feb 5, 2023Feb 5, 2023
    • Github Repository for Tazi et al. : Unified classification and risk-stratification in Acute Myeloid Leukemia. Please check our online tool : https://www.aml-risk-model.com/
      Jupyter Notebook
      5400Updated Aug 9, 2022Aug 9, 2022
    • lsf

      Public
      Snakemake profile for running jobs on an LSF cluster
      Python
      MIT License
      22000Updated Jul 12, 2022Jul 12, 2022
    • Repository of Asimomitis et al. Blood Advances publication: Patient-specific MDS-RS iPSCs define the mis-spliced transcript repertoire and chromatin landscape of SF3B1-mutant HSPCs (https://doi.org/10.1182/bloodadvances.2021006325)
      Jupyter Notebook
      0100Updated Mar 16, 2022Mar 16, 2022
    • TP53 allelic state in MDS
      HTML
      4400Updated Feb 4, 2022Feb 4, 2022
    • 🍪 Cookiecutter template for Class Based Toil pipelines.
      Python
      MIT License
      1400Updated Dec 2, 2021Dec 2, 2021
    • Split bed intervals by estimated read counts from bam index
      Nim
      MIT License
      0921Updated Nov 15, 2021Nov 15, 2021
    • 🤖 A Toil example pipeline created with cookiecutter-toil.
      Python
      MIT License
      1000Updated Sep 8, 2021Sep 8, 2021
    • Split bed intervals by maximum read counts
      Nim
      MIT License
      0900Updated Jul 14, 2021Jul 14, 2021
    • Dockerfile to create a cellranger container
      Dockerfile
      0000Updated Apr 23, 2021Apr 23, 2021