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    168 repositories

    • nanogenome

      Public
      Long-read DNA variant and mobile element analysis
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Apr 18, 2026Apr 18, 2026

    • proteomegenerator3

      Public
      Generate proteogenomics search databases from long-read RNAseq
      Nextflow
      •
      MIT License
      •1•0•0•1•Updated Apr 18, 2026Apr 18, 2026

    • minda

      Public
      Python
      •
      Other
      •4•0•0•0•Updated Apr 10, 2026Apr 10, 2026

    • onboarding

      Public
      1•1•0•1•Updated Apr 8, 2026Apr 8, 2026

    • bamkallisto

      Public
      run kallisto with custom index on pre-aligned bams
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 24, 2026Mar 24, 2026

    • somalierswap

      Public
      Use somalier to check for sample swaps
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 23, 2026Mar 23, 2026

    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      •
      MIT License
      •106•0•0•0•Updated Mar 17, 2026Mar 17, 2026

    • scplover

      Public
      Method scPlOver for inferring DNA content from overlapping fragments in scDNA-seq data
      Python
      •0•0•0•0•Updated Mar 14, 2026Mar 14, 2026

    • scrna_demultiplexing

      Public
      Python
      •
      MIT License
      •1•4•0•0•Updated Mar 2, 2026Mar 2, 2026

    • wgs_analysis

      Public
      Python
      •1•1•0•1•Updated Mar 1, 2026Mar 1, 2026

    • GraffiTE

      Public
      GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read s…
      R
      •
      Other
      •15•0•0•0•Updated Mar 1, 2026Mar 1, 2026

    • hlamp

      Public
      Dynamic evolution of oncogene amplification across 80000 cancer cell genomes
      R
      •0•1•0•0•Updated Feb 13, 2026Feb 13, 2026

    • signals

      Public
      Single Cell Genomes with Allele Specificity
      bioinformaticsrna-seqsingle-cell
      bioinformaticsrna-seqsingle-cell
      R
      •
      Other
      •1•12•2•0•Updated Feb 13, 2026Feb 13, 2026

    • peptidescope

      Public
      visualize MS peptides with transcript structures
      Perl
      •1•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • signals_isabl

      Public
      R
      •0•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • chromoscope

      Public
      Interactive multiscale visualization for structural variation in human genomes
      TypeScript
      •
      MIT License
      •7•0•0•0•Updated Jan 15, 2026Jan 15, 2026

    • spectrum_cfdna_figures

      Public
      Repo to reproduce figures from Williams et al. 2025
      R
      •
      MIT License
      •0•1•0•0•Updated Jan 9, 2026Jan 9, 2026

    • SVChordinator

      Public
      merge, annotate and visualize structural variants
      Python
      •
      Apache License 2.0
      •0•0•0•1•Updated Jan 4, 2026Jan 4, 2026

    • HMMclone

      Public
      Calling copy number in pseudobulk clones
      R
      •
      Other
      •0•3•0•0•Updated Dec 3, 2025Dec 3, 2025

    • driver-concordance

      Public
      A pipeline to process CN and VCF data between paired samples to calculate driver event concordance
      Python
      •0•0•0•0•Updated Nov 13, 2025Nov 13, 2025

    • ORFology

      Public
      protein annotation based on sequence composition
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025

    • tcdo_pg_tools

      Public
      Commandline tools to support proteogenomics analyses at MSK TCDO and beyond
      Python
      •
      Other
      •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025

    • wakcna

      Public
      long-read copy number analysis from phased SVs using Wakhan
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Oct 6, 2025Oct 6, 2025

    • rnasplice

      Public
      rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
      Nextflow
      •
      MIT License
      •37•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • igver

      Public
      Automatically take IGV snapshots
      automationbioinformaticsigv
      automationbioinformaticsigvbioinformatics-tool
      Python
      •
      MIT License
      •1•2•0•0•Updated Aug 11, 2025Aug 11, 2025

    • ArtiCull

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jul 31, 2025Jul 31, 2025

    • bambu-nf

      Public
      nextflow pipeline to run bambu for long-read transcript assembly
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • nanoqc

      Public
      QC and filtering for long-read sequencing data
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jul 17, 2025Jul 17, 2025

    • nfhaplotag

      Public
      Nextflow pipeline for running haplotag software like WhatsHap or longphase
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jun 27, 2025Jun 27, 2025

    • nfphasing

      Public
      Nextflow pipeline for running phasing software like WhatsHap
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Jun 26, 2025Jun 26, 2025
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