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    44 repositories

    • gGnome

      Public
      R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
      R
      •
      MIT License
      •22•41•7•10•Updated Apr 24, 2026Apr 24, 2026

    • gOS-eye

      Public
      A simple live frontend for monitoring nextflow pipeline runs
      Go
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • nf-gos

      Public
      End to end cancer genomics pipeline
      Nextflow
      •
      MIT License
      •3•4•11•0•Updated Apr 23, 2026Apr 23, 2026

    • gosh

      Public
      gOSh (gOS Shell) a CLI for running the nf-gOS pipeline
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • skilift

      Public
      An R interface for loading and modifying PGV datafiles
      R
      •3•0•4•2•Updated Apr 21, 2026Apr 21, 2026

    • gTrack

      Public
      R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework
      R
      •12•17•9•1•Updated Apr 21, 2026Apr 21, 2026

    • gOS

      Public
      Genomic case report
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•10•1•Updated Mar 26, 2026Mar 26, 2026

    • journal-club-hat

      Public
      Sample names from Journal Club
      HTML
      •0•0•0•0•Updated Mar 23, 2026Mar 23, 2026

    • gos-assets

      Public
      Common gOS assets
      HTML
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • multiplicity

      Public
      R
      •
      Other
      •2•1•0•0•Updated Mar 3, 2026Mar 3, 2026

    • bamUtils

      Public
      R
      •5•3•4•0•Updated Feb 12, 2026Feb 12, 2026

    • onenesstwoness

      Public
      Random forest classifier for BRCA1/BRCA2 deletion phenotype classification
      R
      •2•0•0•1•Updated Dec 4, 2025Dec 4, 2025

    • lung_coo_2025

      Public
      HTML
      •
      MIT License
      •0•2•0•0•Updated Nov 11, 2025Nov 11, 2025

    • fishHook

      Public
      R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic cov…
      R
      •10•32•11•0•Updated Oct 29, 2025Oct 29, 2025

    • ssa_polq_2025

      Public
      code and data for SSA-PolQ submission
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 2, 2025Sep 2, 2025

    • alphagenome-cli

      Public
      A command line interface for the Alphagenome API
      Python
      •0•1•0•0•Updated Aug 5, 2025Aug 5, 2025

    • pgv

      Public
      Pan gGnome Viewer
      JavaScript
      •
      MIT License
      •2•10•2•0•Updated Jul 10, 2025Jul 10, 2025

    • nf-jabba

      Public
      R
      •
      MIT License
      •3•15•5•1•Updated May 27, 2025May 27, 2025

    • dryclean

      Public
      Irons out wrinkles in noisy coverage data using robust PCA
      R
      •15•15•6•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

    • fragCounter

      Public
      GC and mappability corrected fragment coverage for paired end whole genome sequencing
      R
      •
      MIT License
      •13•8•18•4•Updated Apr 28, 2025Apr 28, 2025

    • Flow

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

    • skitools

      Public
      General purpose mskilab R tools
      R
      •8•6•1•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
      •26•59•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
      •12•10•6•3•Updated Mar 6, 2025Mar 6, 2025

    • chromunity

      Public
      Discovery of communities in Pore-C concatemers
      R
      •6•15•10•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

    • 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
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