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mgp1000 Public
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
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devgru Public
Developmental environment for GenomicRanges utilities
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dryclean Public
Forked from mskilab-org/drycleanIrons out wrinkles in noisy coverage data using robust PCA
R UpdatedJul 6, 2026 -
myelomaNoncodingGenome Public
Repository for analysis in "Recurrent non-coding mutational hotspots drive chromosomal rearrangement and disease progression in multiple myeloma" from Blaney, P. et al.
HTML MIT License UpdatedJul 1, 2026 -
JaBbA Public
Forked from mskilab-org/JaBbAMIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
R MIT License UpdatedMay 27, 2026 -
gGnome Public
Forked from mskilab-org/gGnomeR API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
R MIT License UpdatedMay 27, 2026 -
rotation-1 Public
BINF 703 Lab Rotation - Expansion of Literature-Based Relationship Extraction Across New Data Sources with Dr. Hongbao Cao
Python UpdatedMay 1, 2026 -
mutsToTrees Public
Workflow to go from mutations to clonal clusters to phylogenetic trees
R UpdatedFeb 28, 2026 -
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CNAqc Public
Forked from caravagnalab/CNAqcClonal and subclonal Copy Number Alteration quality check integrating somatic mutation
R GNU General Public License v3.0 UpdatedSep 19, 2025 -
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Clin-Cancer-Res-29-2023 Public
Repository for analysis in "Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma" from Boyle, E.M., Blaney, P.,…
MIT License UpdatedJul 23, 2025 -
Leukemia-36-2022 Public
Repository for analysis in "Improving prognostic assignment in older adults with multiple myeloma using acquired genetic features, clonal hemopoiesis and telomere length." from Boyle, E.M., William…
R MIT License UpdatedJul 3, 2025 -
Exp-Hematol-Oncol-14-2025 Public
Forked from dgagler/5TGM1-StromalRepository for analysis in "A proinflammatory response and polarized differentiation of stromal elements characterizes the murine myeloma bone marrow niche" from Ghamlouch, H., Gagler, D.C., Blaney…
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Blood.2024028164 Public
Forked from dgagler/WM_scMultiomeAnalysisRepository for analysis in "A multiomic analysis of Waldenström macroglobulinemia defines distinct disease subtypes" from Gagler D., Ghamlouch H., Zhang D., Blaney, P. et al.
Jupyter Notebook UpdatedMay 28, 2025 -
peakCombiner Public
Forked from Novartis/peakCombinerThe fully R based tool peakCombiner is a user-friendly, transparent, modular and customizable package with the purpose to create a consensus peak file from genomic input regions. The aim is to allo…
R Other UpdatedJan 26, 2025 -
pcawgAdditiveVariance Public
Forked from gersteinlab/pcawgAdditiveVarianceAdditive variance of non-coding passengers in Multiple Myeloma
MATLAB UpdatedAug 16, 2024 -
gChain Public
Forked from mskilab-org/gChainR class for representing composable syntenic mappings between coordinates of 'omes and allowing nimble lift-over of genomic features and signals through these mappings within a GenomicRanges based …
R UpdatedJan 5, 2024 -
readsupport Public
Forked from mskilab-org/readsupportComputes read support for arbitrary junctions and contigs for single, paired-end, and linked reads
R MIT License UpdatedJan 5, 2024 -
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battenberg Public
Forked from Wedge-lab/battenbergBattenberg R package for subclonal copynumber estimation
R GNU Affero General Public License v3.0 UpdatedJun 22, 2023 -
mmsig Public
Forked from evenrus/mmsigA method for fitting a known mutational signature reference to mutational catalogues from cancer samples
R Other UpdatedMar 4, 2022