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    19 repositories

    • Microbiome-signatures-CRCbiome

      Public
      This repository contains code for analysis of microbial profiles used to generate results in Birkeland et al.
      R
      •
      MIT License
      •0•0•0•0•Updated Jun 25, 2026Jun 25, 2026

    • skin_microbiome_16S_seq_analyses

      Public
      This repository contains code for pre-processing and analysis of 16S rRNA data from skin swab samples
      microbiomebacteriaphyloseq
      microbiomebacteriaphyloseqqiime2sequencing-analysis
      R
      •
      MIT License
      •0•3•0•0•Updated Jun 20, 2026Jun 20, 2026

    • FIT_metaproteomics

      Public
      Python
      •0•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • CRISPR_interactions

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • sex-differences

      Public
      This repository contains R scripts used to analyze sex-specific microbial differences in the CRCbiome study, with a focus on sex-specific colorectal cancer–asso…
      0•0•0•0•Updated Jan 16, 2026Jan 16, 2026

    • GENOMICON-Seq

      Public
      GENOMICON-Seq is a simulation platform designed for genetic variation exploration through amplicon sequencing and whole exome sequencing (WES). This tool enable…
      C++
      •
      MIT License
      •0•2•0•0•Updated Nov 8, 2025Nov 8, 2025

    • VirMake

      Public
      VirMake is a Snakemake based pipeline that offers viral metagenic data analysis on paired-end data. It offers taxonomic and functional annotation, supports offl…
      Python
      •
      GNU General Public License v3.0
      •2•10•2•0•Updated Oct 24, 2025Oct 24, 2025

    • GENOMICON-Seq_Study_cases

      Public
      R
      •0•0•0•0•Updated Aug 2, 2025Aug 2, 2025

    • VirMake-demo

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

    • LC_biomarkers_Validation

      Public
      This repository contains the scripts used for the external validation of predictive models described in the manuscript "Recommendations for validating omics pre…
      R
      •0•0•0•0•Updated Dec 30, 2024Dec 30, 2024

    • mock_mycobiome

      Public
      Python
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Dec 19, 2024Dec 19, 2024

    • Simulation-and-dimension-reduction-of-shotgun-metagenome-data

      Public
      Scripts, documents, and information related to the Master's thesis "Simulation and dimension reduction of shotgun metagenome data".
      Python
      •0•1•0•0•Updated Nov 15, 2024Nov 15, 2024

    • Phascolarctobacterium_CRC

      Public
      This repository contains code for data analysis used to generate results in the paper Species-level verification of Phascolarctobacterium association to colorec…
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 16, 2024Aug 16, 2024

    • Identification-of-NRPS-PKS-gene-clusters-and-pks-island-in-bacterial-metagenome

      Public
      Python
      •0•0•0•0•Updated May 22, 2024May 22, 2024

    • CRC_Survival_Analysis_ML

      Public
      Hold all the scripts and model implementations used during Emil Jettli's master project on the JanusRNA CRC data
      Python
      •0•0•0•0•Updated May 13, 2024May 13, 2024

    • iSNV_longitudinal_study

      Public
      R scripts used in the study "Changes in intra-host genetic diversity according to lesion severity in longitudinal HPV16 samples"
      R
      •0•0•0•0•Updated Apr 12, 2024Apr 12, 2024

    • world-of-fungi

      Public
      Evaluation of six bioinformatic tools (Kraken2, MetaPhlAn 3 and 4, FindFungi, FunOMIC, HumanMycobiomeScan and EukDetect) for their ability to classify fungal ge…
      Python
      •0•3•0•0•Updated Feb 26, 2024Feb 26, 2024

    • CRCbiome_virome_2023

      Public
      This repository contains code for processing of sequencing data and virus predictions, and data analysis used to generate results in Istvan et al.
      R
      •
      MIT License
      •0•4•0•0•Updated Jan 23, 2024Jan 23, 2024

    • ec-rna

      Public
      R script related to differential expression analysis in the manuscript "Differential levels of circulating RNA prior to endometrial cancer diagnosis"
      R
      •0•0•0•0•Updated Oct 18, 2023Oct 18, 2023
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