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    36 repositories

    • skilift

      Public
      An R interface for loading and modifying PGV datafiles
      R
      •3•0•4•1•Updated Feb 4, 2025Feb 4, 2025

    • nf-gos

      Public
      End to end cancer genomics pipeline
      Nextflow
      •
      MIT License
      •1•1•7•0•Updated Feb 4, 2025Feb 4, 2025

    • gOS

      Public
      Genomic case report
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•9•0•Updated Feb 4, 2025Feb 4, 2025

    • GxG

      Public
      Scalable GenomicRanges based class for storing, manipulating, and querying genomic matrices and pairwise features.
      R
      •
      MIT License
      •6•7•1•0•Updated Jan 30, 2025Jan 30, 2025

    • chromunity

      Public
      Discovery of communities in Pore-C concatemers
      R
      •4•12•6•0•Updated Jan 29, 2025Jan 29, 2025

    • readsupport

      Public
      Computes read support for arbitrary junctions and contigs for single, paired-end, and linked reads
      R
      •
      MIT License
      •2•1•0•0•Updated Jan 29, 2025Jan 29, 2025

    • RSeqLib

      Public
      R interface to SeqLib
      C
      •2•3•0•0•Updated Jan 28, 2025Jan 28, 2025

    • SNVplicity

      Public
      R
      •
      Other
      •1•0•0•0•Updated Jan 18, 2025Jan 18, 2025

    • gTrack

      Public
      R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework
      R
      •12•16•9•1•Updated Jan 7, 2025Jan 7, 2025

    • Flow

      Public
      R-based genomics workflow management
      R
      •6•8•2•1•Updated Dec 11, 2024Dec 11, 2024

    • gUtils

      Public
      Utility functions to extend and optimize GenomicRanges functionality.
      R
      •
      GNU General Public License v2.0
      •10•9•6•3•Updated Oct 22, 2024Oct 22, 2024

    • dryclean

      Public
      Irons out wrinkles in noisy coverage data using robust PCA
      R
      •14•13•2•1•Updated Sep 11, 2024Sep 11, 2024

    • gGnome

      Public
      R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
      R
      •
      MIT License
      •20•39•4•10•Updated Aug 24, 2024Aug 24, 2024

    • fragCounter

      Public
      GC and mappability corrected fragment coverage for paired end whole genome sequencing
      R
      •
      MIT License
      •12•7•15•4•Updated Aug 2, 2024Aug 2, 2024

    • skitools

      Public
      General purpose mskilab R tools
      R
      •8•6•0•1•Updated Jul 2, 2024Jul 2, 2024

    • nf-jabba

      Public
      R
      •
      MIT License
      •3•13•5•1•Updated Jul 2, 2024Jul 2, 2024

    • JaBbA

      Public
      MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
      R
      •
      MIT License
      •26•56•13•1•Updated Jun 5, 2024Jun 5, 2024

    • ggSim

      Public
      comprehensive simulation of whole-genome graphs (coverage, junctions, allelic and SNP phasing)
      R
      •
      Other
      •0•0•0•0•Updated Mar 18, 2024Mar 18, 2024

    • pgv

      Public
      Pan gGnome Viewer
      JavaScript
      •
      MIT License
      •2•10•2•0•Updated Feb 12, 2024Feb 12, 2024

    • case-report-api

      Public
      The API service to facilitate the case-report frontend application
      Ruby
      •
      MIT License
      •0•0•0•0•Updated Jan 10, 2024Jan 10, 2024

    • pgv-api

      Public
      The API service to facilitate the pgv frontend application
      MIT License
      •0•0•0•0•Updated Jan 6, 2024Jan 6, 2024

    • homeology

      Public
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Dec 4, 2023Dec 4, 2023

    • loosends

      Public
      Loose ends in cancer genome structure
      R
      •
      MIT License
      •2•2•1•0•Updated Aug 17, 2023Aug 17, 2023

    • FlowExample

      Public
      Using Flow within NYGC Mskilab
      HTML
      •0•0•0•0•Updated Jun 26, 2023Jun 26, 2023

    • .github

      Public
      0•0•0•0•Updated Jun 14, 2023Jun 14, 2023

    • ffTrack

      Public
      GenomicRanges based R class for fast, out-of-core memory access and storage of numeric and character data that is a function of genomic position.
      R
      •
      MIT License
      •0•0•1•0•Updated Jan 30, 2023Jan 30, 2023

    • skidb

      Public
      Reference data utilities for mskilab
      R
      •1•1•0•0•Updated Jan 28, 2023Jan 28, 2023

    • gGnome.js

      Public
      JavaScript
      •
      MIT License
      •5•26•0•2•Updated Dec 9, 2022Dec 9, 2022

    • fishHook

      Public
      R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.
      R
      •9•27•9•0•Updated Dec 5, 2022Dec 5, 2022

    • gChain

      Public
      R 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 framework.
      R
      •2•0•0•3•Updated Dec 4, 2022Dec 4, 2022