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    142 repositories

    • igver

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

    • onboarding

      Public
      1•1•0•1•Updated Mar 14, 2025Mar 14, 2025

    • SVChordinator

      Public
      merge, annotate and visualize structural variants
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 14, 2025Mar 14, 2025

    • alhena-docker

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

    • ArtiCull

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

    • spectrum-tme

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

    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      •
      MIT License
      •91•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • SCLC_MET

      Public
      Scripts and notebooks analyzing single cell omics data.
      Jupyter Notebook
      •0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

    • proteomegenerator-smk

      Public
      Snakemake workflow for proteomegenerator Isabl app
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 17, 2025Feb 17, 2025

    • transdecoder-smk

      Public
      snakemake pipeline for transdecoder
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 17, 2025Feb 17, 2025

    • bambu-smk

      Public
      Snakemake workflow for transcript assembly with Bambu
      R
      •
      MIT License
      •0•0•0•0•Updated Feb 14, 2025Feb 14, 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 Feb 14, 2025Feb 14, 2025

    • rustbam

      Public
      Rust-powered BAM depth extraction with Python bindings
      rustbioinformaticsgenomicsbampyo3
      Rust
      •
      MIT License
      •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • hairloom

      Public
      A tool for analyzing split reads (focusing on long-read data)
      bioinformaticsnanoporegenomics
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • ontmont

      Public
      ONT split read analysis
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 16, 2025Jan 16, 2025

    • signals

      Public
      Single Cell Genomes with Allele Specificity
      bioinformaticsrna-seqsingle-cell
      R
      •
      Other
      •1•8•2•0•Updated Jan 7, 2025Jan 7, 2025

    • alhena_igo

      Public
      Alhena loader for IGO
      Python
      •
      MIT License
      •0•0•0•1•Updated Dec 20, 2024Dec 20, 2024

    • gdan-sv-consensus

      Public
      Getting GDAN SV consensus based on bedpe files
      Python
      •0•1•0•0•Updated Dec 10, 2024Dec 10, 2024

    • wgs_analysis

      Public
      Python
      •1•1•0•1•Updated Nov 27, 2024Nov 27, 2024

    • scrna_demultiplexing

      Public
      Python
      •
      MIT License
      •1•4•0•0•Updated Nov 18, 2024Nov 18, 2024

    • cellranger_utils

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • doubleTime

      Public
      doubleTime is a method to estimate the timing of whole-genome doubling event(s) on a clone tree using SNVs
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Nov 15, 2024Nov 15, 2024

    • wgs

      Public
      Whole genome workflows
      Python
      •6•12•0•0•Updated Nov 9, 2024Nov 9, 2024

    • xengsort-smk

      Public
      Snakemake pipeline for xengsort
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • pypeliner

      Public
      Python
      •
      GNU General Public License v3.0
      •5•2•0•0•Updated Oct 16, 2024Oct 16, 2024

    • alhenaloader

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated Sep 26, 2024Sep 26, 2024

    • scdna_replication_paper

      Public
      Investigating DNA replication dynamics using DLP data
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • scdna_replication_tools

      Public
      Tools for assigning S-phase cells to clones and inferring single-cell replication timing (scRT) profiles
      Jupyter Notebook
      •
      MIT License
      •1•1•1•0•Updated Jul 29, 2024Jul 29, 2024

    • medicc2_nextflow

      Public
      Medicc2 nextflow pipeline
      Nextflow
      •1•1•0•2•Updated Jul 25, 2024Jul 25, 2024

    • bulk-illumina-rnaseq

      Public
      RNA seq analysis pipeline for alignment and quantification of bulk illumina data
      Nextflow
      •
      MIT License
      •747•0•0•0•Updated Jun 29, 2024Jun 29, 2024