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    85 repositories

    • phylogeny-of-single-cells

      Public
      snakemake workflow for the phylogenetic reconstruction of single cell lineages from multiple displacement amplified single cell DNAseq
      Python
      •
      MIT License
      •1•0•0•1•Updated Dec 12, 2024Dec 12, 2024

    • ChemLM

      Public
      Jupyter Notebook
      •
      Academic Free License v3.0
      •0•1•0•0•Updated Dec 12, 2024Dec 12, 2024

    • mag

      Public
      Best practice pipeline for assembly and binning of metagenomes based on CAMI2 challenge, adapted from nf-core/mag
      Nextflow
      •
      MIT License
      •111•1•2•0•Updated Dec 11, 2024Dec 11, 2024

    • Broker4Microbiota

      Public
      Django App for collection and storage of sequencing orders for the sequencing facility
      JavaScript
      •0•0•2•0•Updated Dec 10, 2024Dec 10, 2024

    • Corona_Variant_Scoring

      Public
      Method to score circulating SARS-CoV-2 lineages on their potential antigenicity
      vaccinessars-cov-2antigenicityimmune-escape
      HTML
      •
      Other
      •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • AMR_benchmarking

      Public
      Python
      •
      MIT License
      •0•3•0•0•Updated Nov 29, 2024Nov 29, 2024

    • corona_lineage_dynamics

      Public
      SDPlots scripts for the coverage server
      C++
      •
      Other
      •0•1•2•0•Updated Nov 24, 2024Nov 24, 2024

    • seminar-dlmb-2024-winter-public

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Oct 14, 2024Oct 14, 2024

    • AMR_prediction_pipeline

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • epitope-prediction

      Public
      Python
      •
      GNU General Public License v3.0
      •11•15•0•2•Updated Jun 10, 2024Jun 10, 2024

    • AntigenicTreeTools

      Public
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 21, 2024May 21, 2024

    • fastml

      Public
      A copy of https://github.com/AidanDelaney/fastml with errors fixed
      C++
      •0•0•0•0•Updated May 17, 2024May 17, 2024

    • covid-germany-mcmc

      Public
      SARS-CoV-2 lineage importations and spread are reduced after nonpharmaceutical interventions in phylogeographic analyses
      HTML
      •0•2•0•0•Updated Apr 11, 2024Apr 11, 2024

    • taxprofiler

      Public
      Highly parallelised multi-taxonomic profiling of shotgun metagenomic data
      Nextflow
      •
      MIT License
      •36•0•0•0•Updated Apr 3, 2024Apr 3, 2024

    • corona_protein_dynamics

      Public
      Mutation dynamics analysis of SARS-Cov-2 S-protein based on phylogenetics and statistics
      Python
      •
      Other
      •0•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • RiboDetector

      Public
      Accurate and rapid RiboRNA sequences Detector based on deep learning
      Python
      •
      GNU General Public License v3.0
      •16•99•7•0•Updated Jan 10, 2024Jan 10, 2024

    • ngs_form

      Public
      HTML
      •0•0•0•0•Updated Nov 21, 2023Nov 21, 2023

    • covid-germany-mcmc-one-tree-public

      Public
      R
      •0•0•0•0•Updated Oct 10, 2023Oct 10, 2023

    • covid-germany-mcmc-phylogeo-tools

      Public
      A phylogeo-tools for covid-germany-mcmc
      C++
      •0•0•0•0•Updated Oct 10, 2023Oct 10, 2023

    • Haploflow

      Public
      C++
      •
      GNU General Public License v3.0
      •3•29•6•0•Updated Sep 21, 2023Sep 21, 2023

    • epitope-prediction-paper

      Public
      Data and results for the EpitopeVec paper
      Python
      •3•5•0•2•Updated Jul 6, 2023Jul 6, 2023

    • hcv-mds

      Public
      Neutralization maps for HCV data
      Python
      •0•0•2•2•Updated Jul 6, 2023Jul 6, 2023

    • lotus

      Public
      Scripts related to the Lotus japonicus root microbiota manuscript Zgadzaj, Garrido-Oter et al., 2016
      R
      •7•0•0•1•Updated Jul 3, 2023Jul 3, 2023

    • scelestial

      Public
      0•0•0•0•Updated Jun 10, 2023Jun 10, 2023

    • Quasimodo

      Public
      QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture
      benchmarkingmetagenomicsviral-genomics
      C++
      •
      GNU General Public License v3.0
      •3•13•1•0•Updated Sep 22, 2022Sep 22, 2022

    • scelestial-paper-materials-devel

      Public
      The lineage tree reconstruction method based on Steiner tree problem - dataset and test scripts for the paper (development version)
      C++
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated May 30, 2022May 30, 2022

    • Haploflow_supplementary

      Public
      Helper scripts and other supplementary material for Haploflow
      Python
      •0•0•1•0•Updated May 6, 2022May 6, 2022

    • snakemake-workflow-univec-removal

      Public
      A small Snakemake workflow to remove contaminating vector sequences from raw sequencing data using UniVec.
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 3, 2022Feb 3, 2022

    • sankoff

      Public
      C++
      •0•0•0•0•Updated Dec 31, 2021Dec 31, 2021

    • which_tree

      Public
      Testing of phylogenetic inference methods
      R
      •
      GNU General Public License v2.0
      •3•0•0•0•Updated Oct 19, 2021Oct 19, 2021