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    14 repositories

    • VirMake-demo

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Feb 10, 2025Feb 10, 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 offline running and support for HPC cluster execution. It is made for Linux based systems and has been tested on SLURM cluster execution.
      Python
      •
      GNU General Public License v3.0
      •1•7•2•0•Updated Jan 27, 2025Jan 27, 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 prediction models: Insights from a lung cancer RNA biomarker study".
      R
      •0•0•0•0•Updated Dec 30, 2024Dec 30, 2024

    • mock_mycobiome

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

    • skin_microbiome_16S_seq_analyses

      Public
      This repository contains code for pre-processing and analysis of 16S rRNA data used to generate results in the paper "Skin bacterial community dynamics of hands and forearms before and after military field exercise".
      microbiomebacteriaphyloseqqiime2sequencing-analysis
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 13, 2024Dec 13, 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

    • GENOMICON-Seq

      Public
      GENOMICON-Seq is a simulation platform designed for genetic variation exploration through amplicon sequencing and whole exome sequencing (WES). This tool enables users to create virtual DNA samples with adjustable mutation frequencies, helping to understand the effects of simulated library prep biases and errors on mutation detection.
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 17, 2024Aug 17, 2024

    • Phascolarctobacterium_CRC

      Public
      R
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      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 genomes
      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•2•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