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@koesterlab Bioinformatics and Computational Oncology (Koesterlab)

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    34 repositories

    • koesterlab.github.io

      Public
      HTML
      •0•0•0•0•Updated Feb 27, 2025Feb 27, 2025

    • data-science-for-bioinfo

      Public
      A collection of resources for data scientists (not only) in bioinformatics
      MIT License
      •3•7•0•1•Updated Feb 21, 2025Feb 21, 2025

    • nature-datavzrd-report-workflow

      Public
      Python
      •0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

    • texp

      Public
      Rust
      •
      MIT License
      •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • remail

      Public
      Python
      •0•1•0•2•Updated Jan 31, 2025Jan 31, 2025

    • locosopa

      Public
      A github action for creating software homepages with low code.
      Python
      •
      MIT License
      •1•1•0•0•Updated Jan 29, 2025Jan 29, 2025

    • srptn

      Public
      SeRPentine - the Snakemake research platform
      Python
      •0•3•0•0•Updated Jan 29, 2025Jan 29, 2025

    • setup-slurm-action

      Public
      A github action to setup a small SLURM cluster for testing purposes.
      MIT License
      •2•11•2•2•Updated Dec 23, 2024Dec 23, 2024

    • koesterlab-workstation-ansible

      Public
      MIT License
      •2•0•0•2•Updated Dec 13, 2024Dec 13, 2024

    • datavzrd-chatbot

      Public
      A chatbot to create datavzrd configs
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • rossi-ips-dmr

      Public
      Calling and plotting of differentially methylated regions between two or more biological samples in BAM format
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • ngs-test-data

      Public
      A workflow for creating small NGS test data sets, useful for continuous integration.
      Python
      •
      MIT License
      •14•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • teaching-data-analysis-visualization-reproducibility

      Public
      Course on data analysis, visualization and reproducibility at the faculty of medicine
      Python
      •0•0•0•0•Updated Aug 19, 2024Aug 19, 2024

    • conda-inject

      Public
      Helper functions for injecting a conda environment into the current python environment (by modifying sys.path, without actually changing the current python environment)
      Python
      •
      MIT License
      •0•1•0•0•Updated May 27, 2024May 27, 2024

    • praxisprojekt-rust-ss-2024

      Public
      MIT License
      •0•0•0•0•Updated Mar 10, 2024Mar 10, 2024

    • Feature-extraction-from-random-forest

      Public
      A repo to extract imporant features and its associated features from a random forest
      random-forestfeature-extraction
      Python
      •0•0•0•0•Updated Dec 1, 2023Dec 1, 2023

    • microphaser

      Public
      softwarevariant-callingphasing
      Rust
      •
      MIT License
      •2•12•4•1•Updated Sep 7, 2023Sep 7, 2023

    • rna-seq-kallisto-sleuth

      Public
      Python
      •
      MIT License
      •45•0•0•0•Updated Aug 10, 2023Aug 10, 2023

    • voyager

      Public
      Visualization Tool for Data Exploration
      TypeScript
      •
      Other
      •178•0•0•5•Updated Jul 3, 2023Jul 3, 2023

    • calfreeslots

      Public
      A small command line utility for printing free calendar slots in the coming days
      Python
      •0•6•0•0•Updated Sep 26, 2022Sep 26, 2022

    • HLA-simulation-evaluation

      Public
      Python
      •0•0•0•0•Updated Mar 24, 2022Mar 24, 2022

    • fgbio

      Public
      Tools for working with genomic and high throughput sequencing data.
      Scala
      •
      MIT License
      •70•0•0•1•Updated Mar 1, 2022Mar 1, 2022

    • ngs-fastq-to-cram

      Public
      Snakemake workflow for converting FASTQ files to self-contained CRAM files with maximum lossless compression.
      Python
      •
      MIT License
      •0•1•0•0•Updated Dec 16, 2021Dec 16, 2021

    • dna-seq-gatk-variant-calling

      Public
      This Snakemake pipeline implements the GATK best-practices workflow
      Python
      •
      MIT License
      •145•2•0•0•Updated Apr 9, 2021Apr 9, 2021

    • snakemake-gitpod-template

      Public template
      A gitpod template for developing a Snakemake workflow
      0•0•0•0•Updated Mar 3, 2021Mar 3, 2021

    • single-cell-rna-seq

      Public
      A single cell RNA-seq workflow following http://dx.doi.org/10.12688/f1000research.9501.2
      R
      •
      MIT License
      •44•0•0•1•Updated Jan 14, 2021Jan 14, 2021

    • genomes

      Public
      web-based genome viewer
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jun 13, 2020Jun 13, 2020

    • chm-synthetic-tumor-normal

      Public
      Creating a synthetic tumor/normal sample pair from CHM1/CHM13 haploid cell lines.
      Python
      •0•0•0•0•Updated Jan 29, 2020Jan 29, 2020

    • autoref

      Public
      A snakemake workflow for downloading reference data from, e.g. aws-igenomes
      Python
      •0•0•0•0•Updated Nov 6, 2019Nov 6, 2019

    • go_term_p_value_aggregation

      Public
      Code to aggregate sleuth differential expression p-values of individual transcripts to GO terms. (WIP!)
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 19, 2019Jul 19, 2019