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    41 repositories

    • gOS

      Public
      Genomic case report
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•10•0•Updated Jul 4, 2025Jul 4, 2025

    • nf-gos

      Public
      End to end cancer genomics pipeline
      Nextflow
      •
      MIT License
      •2•1•10•0•Updated Jul 1, 2025Jul 1, 2025

    • gosh

      Public
      gOSh (gOS Shell) a CLI for running the nf-gOS pipeline
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 1, 2025Jul 1, 2025

    • multiplicity

      Public
      R
      •
      Other
      •1•1•0•1•Updated Jun 27, 2025Jun 27, 2025

    • lung_coo_2025

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

    • skilift

      Public
      An R interface for loading and modifying PGV datafiles
      R
      •3•0•4•0•Updated Jun 16, 2025Jun 16, 2025

    • gos-assets

      Public
      Common gOS assets
      HTML
      •0•0•0•0•Updated Jun 5, 2025Jun 5, 2025

    • gGnome

      Public
      R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
      R
      •
      MIT License
      •21•40•7•10•Updated May 30, 2025May 30, 2025

    • nf-jabba

      Public
      R
      •
      MIT License
      •3•13•5•1•Updated May 27, 2025May 27, 2025

    • dryclean

      Public
      Irons out wrinkles in noisy coverage data using robust PCA
      R
      •14•15•3•1•Updated May 14, 2025May 14, 2025

    • GxG

      Public
      Scalable GenomicRanges based class for storing, manipulating, and querying genomic matrices and pairwise features.
      R
      •
      MIT License
      •7•7•2•0•Updated May 7, 2025May 7, 2025

    • ssa_polq_2025

      Public
      code and data for SSA-PolQ submission
      R
      •
      MIT License
      •0•0•0•0•Updated May 6, 2025May 6, 2025

    • fragCounter

      Public
      GC and mappability corrected fragment coverage for paired end whole genome sequencing
      R
      •
      MIT License
      •13•7•17•4•Updated Apr 28, 2025Apr 28, 2025

    • bamUtils

      Public
      R
      •5•3•4•0•Updated Apr 26, 2025Apr 26, 2025

    • Flow

      Public
      R-based genomics workflow management
      R
      •6•8•2•0•Updated Apr 24, 2025Apr 24, 2025

    • onenesstwoness

      Public
      Random forest classifier for BRCA1/BRCA2 deletion phenotype classification
      R
      •1•0•0•0•Updated Apr 18, 2025Apr 18, 2025

    • skitools

      Public
      General purpose mskilab R tools
      R
      •8•6•0•1•Updated Apr 15, 2025Apr 15, 2025

    • JaBbA

      Public
      MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
      R
      •
      MIT License
      •27•57•15•1•Updated Mar 23, 2025Mar 23, 2025

    • 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•1•Updated Mar 21, 2025Mar 21, 2025

    • gUtils

      Public
      Utility functions to extend and optimize GenomicRanges functionality.
      R
      •
      GNU General Public License v2.0
      •11•9•6•3•Updated Mar 6, 2025Mar 6, 2025

    • chromunity

      Public
      Discovery of communities in Pore-C concatemers
      R
      •5•12•9•0•Updated Feb 12, 2025Feb 12, 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

    • 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

    • 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
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