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    • Long-read DNA variant and mobile element analysis
      Nextflow
      MIT License
      2000Updated Apr 18, 2026Apr 18, 2026
    • Generate proteogenomics search databases from long-read RNAseq
      Nextflow
      MIT License
      1001Updated Apr 18, 2026Apr 18, 2026
    • minda

      Public
      Python
      Other
      4000Updated Apr 10, 2026Apr 10, 2026
    • 1101Updated Apr 8, 2026Apr 8, 2026
    • run kallisto with custom index on pre-aligned bams
      Nextflow
      MIT License
      0000Updated Mar 24, 2026Mar 24, 2026
    • Use somalier to check for sample swaps
      Nextflow
      MIT License
      0000Updated Mar 23, 2026Mar 23, 2026
    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      MIT License
      106000Updated Mar 17, 2026Mar 17, 2026
    • scplover

      Public
      Method scPlOver for inferring DNA content from overlapping fragments in scDNA-seq data
      Python
      0000Updated Mar 14, 2026Mar 14, 2026
    • Python
      MIT License
      1400Updated Mar 2, 2026Mar 2, 2026
    • Python
      1101Updated 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
      15000Updated Mar 1, 2026Mar 1, 2026
    • hlamp

      Public
      Dynamic evolution of oncogene amplification across 80000 cancer cell genomes
      R
      0100Updated Feb 13, 2026Feb 13, 2026
    • signals

      Public
      Single Cell Genomes with Allele Specificity
      R
      Other
      11220Updated Feb 13, 2026Feb 13, 2026
    • visualize MS peptides with transcript structures
      Perl
      1000Updated Feb 11, 2026Feb 11, 2026
    • R
      0000Updated Feb 3, 2026Feb 3, 2026
    • Interactive multiscale visualization for structural variation in human genomes
      TypeScript
      MIT License
      7000Updated Jan 15, 2026Jan 15, 2026
    • Repo to reproduce figures from Williams et al. 2025
      R
      MIT License
      0100Updated Jan 9, 2026Jan 9, 2026
    • merge, annotate and visualize structural variants
      Python
      Apache License 2.0
      0001Updated Jan 4, 2026Jan 4, 2026
    • HMMclone

      Public
      Calling copy number in pseudobulk clones
      R
      Other
      0300Updated Dec 3, 2025Dec 3, 2025
    • A pipeline to process CN and VCF data between paired samples to calculate driver event concordance
      Python
      0000Updated Nov 13, 2025Nov 13, 2025
    • ORFology

      Public
      protein annotation based on sequence composition
      Nextflow
      MIT License
      0000Updated Oct 20, 2025Oct 20, 2025
    • Commandline tools to support proteogenomics analyses at MSK TCDO and beyond
      Python
      Other
      0000Updated Oct 20, 2025Oct 20, 2025
    • wakcna

      Public
      long-read copy number analysis from phased SVs using Wakhan
      Nextflow
      MIT License
      0000Updated Oct 6, 2025Oct 6, 2025
    • rnasplice

      Public
      rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
      Nextflow
      MIT License
      37000Updated Aug 25, 2025Aug 25, 2025
    • igver

      Public
      Automatically take IGV snapshots
      Python
      MIT License
      1200Updated Aug 11, 2025Aug 11, 2025
    • ArtiCull

      Public
      Jupyter Notebook
      MIT License
      0100Updated Jul 31, 2025Jul 31, 2025
    • bambu-nf

      Public
      nextflow pipeline to run bambu for long-read transcript assembly
      Nextflow
      MIT License
      0000Updated Jul 28, 2025Jul 28, 2025
    • nanoqc

      Public
      QC and filtering for long-read sequencing data
      Nextflow
      MIT License
      0000Updated Jul 17, 2025Jul 17, 2025
    • Nextflow pipeline for running haplotag software like WhatsHap or longphase
      Nextflow
      MIT License
      0000Updated Jun 27, 2025Jun 27, 2025
    • nfphasing

      Public
      Nextflow pipeline for running phasing software like WhatsHap
      Nextflow
      MIT License
      0100Updated Jun 26, 2025Jun 26, 2025
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