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    158 repositories

    • ArtiCull

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

    • ORFology

      Public
      protein annotation based on sequence composition
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jul 30, 2025Jul 30, 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

    • proteomegenerator3

      Public
      Generate proteogenomics search databases from long-read RNAseq
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • nanoqc

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

    • HMMclone

      Public
      Calling copy number in pseudobulk clones
      R
      •
      Other
      •0•1•0•0•Updated Jul 11, 2025Jul 11, 2025

    • tcdo_pg_tools

      Public
      Commandline tools to support proteogenomics analyses at MSK TCDO and beyond
      Python
      •
      Other
      •0•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • spectrum_cfdna_figures

      Public
      Repo to reproduce figures from Williams et al. 2025
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 3, 2025Jul 3, 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

    • proteinannotator

      Public
      Custom version of nf-core/proteinannotator workflow
      Nextflow
      •
      MIT License
      •8•0•0•0•Updated Jun 25, 2025Jun 25, 2025

    • nanoquant

      Public
      quantify expression & splicing in bulk, ONT RNAseq data
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jun 16, 2025Jun 16, 2025

    • onboarding

      Public
      1•1•0•1•Updated Jun 13, 2025Jun 13, 2025

    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      •
      MIT License
      •98•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • medicc2_nextflow

      Public
      Medicc2 nextflow pipeline
      Nextflow
      •1•1•0•2•Updated May 22, 2025May 22, 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 May 20, 2025May 20, 2025

    • bulk-rnaseq

      Public
      Pipeline for processing bulk RNAseq data
      Python
      •0•0•0•0•Updated May 19, 2025May 19, 2025

    • bambu-smk

      Public
      Snakemake workflow for transcript assembly with Bambu
      R
      •
      MIT License
      •0•0•0•0•Updated May 18, 2025May 18, 2025

    • nfdorado

      Public
      Nextflow Dorado Pipeline
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated May 16, 2025May 16, 2025

    • spectrum_wgd_paper

      Public
      Analysis repo for the SPECTRUM WGD paper
      HTML
      •0•2•0•0•Updated May 15, 2025May 15, 2025

    • egfr_nucseq

      Public
      Code for the EGFR nucseq paper
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 12, 2025May 12, 2025

    • spectrum-tme

      Public
      Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"
      R
      •8•22•1•0•Updated May 10, 2025May 10, 2025

    • peptidescope

      Public
      visualize MS peptides with transcript structures
      Perl
      •1•0•0•0•Updated May 6, 2025May 6, 2025

    • SCLC_MET

      Public
      Scripts and notebooks analyzing single cell omics data.
      Jupyter Notebook
      •0•0•0•0•Updated Apr 21, 2025Apr 21, 2025

    • SVChordinator

      Public
      merge, annotate and visualize structural variants
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 8, 2025Apr 8, 2025

    • minda

      Public
      Python
      •
      Other
      •5•0•0•0•Updated Apr 8, 2025Apr 8, 2025

    • hairloom

      Public
      A tool for analyzing split reads (focusing on long-read data)
      bioinformaticsnanoporegenomics
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 8, 2025Apr 8, 2025

    • wgs_analysis

      Public
      Python
      •1•1•0•1•Updated Apr 7, 2025Apr 7, 2025

    • igver

      Public
      Automatically take IGV snapshots
      automationbioinformaticsigvbioinformatics-tool
      Python
      •
      MIT License
      •1•1•0•1•Updated Mar 21, 2025Mar 21, 2025

    • alhena-docker

      Public
      Docker files for Alhena
      Dockerfile
      •0•0•0•1•Updated Mar 12, 2025Mar 12, 2025