Elli Papaemmanuil Lab
We study the role of acquired mutations in cancer development and how these determine clinical phenotype and response to therapy.
New York, USA
Pinned Repositories
cookiecutter-toil
🍪 Cookiecutter template for Class Based Toil pipelines.
Gao_NC_CH
Code and Data for Gao et al., Nature Communications 2021
ipssm
Molecular International Prognostic Scoring System IPSS-M for Myelodysplastic Syndromes
istack
Icon stack bars with group coloring
mergeSVvcf
Python package and routines for merging SV VCF files
register_apps
👾 Register versioned toil container pipelines in a bin directory as singularity images.
split_bed_by_index
Split bed intervals by estimated read counts from bam index
split_bed_by_reads
Split bed intervals by maximum read counts
toil_cnacs
toil wrapper for CNACS
toil_container
:whale: Toil + Docker and Singularity.
Elli Papaemmanuil Lab's Repositories
papaemmelab/split_bed_by_index
Split bed intervals by estimated read counts from bam index
papaemmelab/split_bed_by_reads
Split bed intervals by maximum read counts
papaemmelab/toil_container
:whale: Toil + Docker and Singularity.
papaemmelab/ipssm
Molecular International Prognostic Scoring System IPSS-M for Myelodysplastic Syndromes
papaemmelab/mergeSVvcf
Python package and routines for merging SV VCF files
papaemmelab/Gao_NC_CH
Code and Data for Gao et al., Nature Communications 2021
papaemmelab/IPSSMstudy
IPSS-M study
papaemmelab/register_apps
👾 Register versioned toil container pipelines in a bin directory as singularity images.
papaemmelab/Shukla_Levine_Gundem
Data for Shukla, Levine, Gundem et al.
papaemmelab/cookiecutter-toil
🍪 Cookiecutter template for Class Based Toil pipelines.
papaemmelab/MDS-TP53-state
TP53 allelic state in MDS
papaemmelab/Tazi_NatureC_AML
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/
papaemmelab/isabl_cli
🤖 isabl Command Line Client and SDK.
papaemmelab/Domenico_Asimomitis_ICML_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
papaemmelab/MDS_SF3B1_iPSC
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)
papaemmelab/toil_hla
🧬 Toil workflow for HLA typing tools.
papaemmelab/AnnotSV
Fork from AnnotSV
papaemmelab/Asimomitis_ACM_2023
ICBBB 2023: Predicting Single Cell Genotypes from Single Cell Expression Profiles in AML Using Deep Learning
papaemmelab/cnvkit
Copy number variant detection from targeted DNA sequencing
papaemmelab/Complex_Oncoprint
papaemmelab/docker-cellranger
Dockerfile to create a cellranger container
papaemmelab/docker-hmftools
🐳 Docker container with several HMF tools installed
papaemmelab/gundem_et_al_Nature_Genetics_2023
papaemmelab/hileup
horizontal pileup
papaemmelab/ipssm-api
API and CLI for IPSS-M
papaemmelab/lsf
Snakemake profile for running jobs on an LSF cluster
papaemmelab/nf-purple
Nextflow Pipeline to run Purple from HmfTools
papaemmelab/papaemmelab
👩🏻🔬 The Papaemmanuil Lab Website
papaemmelab/toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
papaemmelab/toil_example
:robot: A Toil example pipeline created with cookiecutter-toil.