Skip to content

@acg-team Applied Computational Genomics Team

Change the repository type filter

All

    Repositories list

    52 repositories

    • Bioinfo4B

      Public
      Jupyter Notebook
      •2•6•0•0•Updated Feb 26, 2026Feb 26, 2026

    • strvcf_annotator

      Public
      Tool that adds STR (Short Tandem Repeat) information to VCF files.
      bioinformaticsgenomicsvcfshort-tandem-repeats
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 26, 2026Feb 26, 2026

    • rust-phylo

      Public
      Phylo library in Rust
      Rust
      •
      Apache License 2.0
      •2•11•42•5•Updated Feb 24, 2026Feb 24, 2026

    • nextflow-pvacseq

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

    • STR_population_structure

      Public
      High-resolution population structure inference using genome-wide STR variations.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • PKS-analysis-pipeline

      Public
      This repository contains the nextflow pipeline for analysing polyketide synthase sequences
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • str_mut_signatures

      Public
      Extract STR signatures from annotated VCF
      vcfcancer-genomicsmutational-signaturesshort-tandem-repeats
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 20, 2026Jan 20, 2026

    • data_acquisition_pipeline

      Public
      Data acquisition pipeline for phylogenetic inference benchmarking.
      Python
      •0•0•0•0•Updated Jan 4, 2026Jan 4, 2026

    • CO5

      Public
      Generative AI in Life Science- Winter 2026
      0•0•0•0•Updated Dec 7, 2025Dec 7, 2025

    • nuclei-graph-mil

      Public
      A Snakemake workflow for whole-slide image (WSI) preprocessing, feature extraction, batch correction, cell segmentation, graph construction, and attention-based…
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 28, 2025Nov 28, 2025

    • shared_files

      Public
      Repository with shared files
      0•0•0•0•Updated Oct 21, 2025Oct 21, 2025

    • JATI

      Public
      JATI: Joint Alignment and Tree Inference
      Rust
      •
      Apache License 2.0
      •0•2•0•1•Updated Oct 14, 2025Oct 14, 2025

    • Bachelor_Thesis_Luigi_Palese_Pipeline_development_for_10X_single_cell

      Public
      Pipeline_development_for_10X_single_cell_pre_processing_analysis_and_visualization
      R
      •1•0•0•0•Updated Jul 3, 2025Jul 3, 2025

    • ConSTRain

      Public
      A short tandem repeat variant caller that incorporates copy number information
      Rust
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Jul 2, 2025Jul 2, 2025

    • multicancer_STR

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • mucin-cancer-analysis

      Public
      Analysis of mucin gene expression and its role in cancer.
      0•0•0•0•Updated May 22, 2025May 22, 2025

    • mutation-tme-crc

      Public
      Machine learning analysis of genetic mutations (STRs, SNPs, indels) and tumor microenvironment (TME) features in colorectal cancer using TCGA data.
      0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • tmb_crc_scripts

      Public
      0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

    • ConSTRain-analyses

      Public
      Genotyping of STR loci that are located in copy number alterations or polyploid organisms
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 7, 2025Jan 7, 2025

    • STR-density

      Public
      Scripts and background to determine short tandem repeat (STR) densities in genes and genomes
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Nov 27, 2024Nov 27, 2024

    • str_project

      Public
      Expression Analysis across different Colorectal Tumors
      R
      •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

    • Indel-Pattern-Analysis-HIV

      Public
      Python
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • webSTR-API

      Public
      WebSTR-API: programmatic access to WebSTR, database of Human genome-wide variation in Short Tandem Repeats (STRs)
      apibioinformaticsgenomicstandem-repeats
      Python
      •
      MIT License
      •4•6•0•1•Updated Aug 6, 2024Aug 6, 2024

    • single-char-indel-ASR-preserves-long-indels

      Public
      This repository includes the scripts used for analysis investigating the dynamics of indels in mammalian orthologous proteins and the examination of the ancestr…
      indelsancestral-sequence-reconstruction
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•1•Updated Jul 31, 2024Jul 31, 2024

    • Bioinfo4B-STR

      Public
      Short tandem repeat project for the course "Bioinformatics for Beginners"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 27, 2024May 27, 2024

    • Selection-in-Genes-Course

      Public
      GNU General Public License v3.0
      •1•0•0•0•Updated May 21, 2024May 21, 2024

    • acg-team.github.io

      Public
      0•0•0•0•Updated Feb 8, 2024Feb 8, 2024

    • rust-indelMaP

      Public
      IndelMaP algorithm implementation in Rust
      Rust
      •
      MIT License
      •0•1•0•0•Updated Nov 16, 2023Nov 16, 2023

    • IndelViewer

      Public
      Indel viewer software for ARPIP
      visualizationpythonphylogenyancestral-state-reconstruction
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 9, 2023Nov 9, 2023

    • indelMaP

      Public
      Python
      •2•5•0•1•Updated Nov 7, 2023Nov 7, 2023