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@acg-team Applied Computational Genomics Team

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    50 repositories

    • rust-phylo

      Public
      Phylo library in Rust
      Rust
      •
      Apache License 2.0
      •2•11•27•3•Updated Jan 7, 2026Jan 7, 2026

    • str_mut_signatures

      Public
      Extract STR signatures from annotated VCF
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 26, 2025Dec 26, 2025

    • CO5

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

    • strvcf_annotator

      Public
      Tool that adds STR (Short Tandem Repeat) information to VCF files.
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 5, 2025Dec 5, 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 ml.
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 28, 2025Nov 28, 2025

    • STR_population_structure

      Public
      High-resolution population structure inference using genome-wide STR variations.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 26, 2025Nov 26, 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

    • nextflow-pvacseq

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Sep 25, 2025Sep 25, 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

    • Bioinfo4B

      Public
      Jupyter Notebook
      •2•5•0•0•Updated Apr 11, 2025Apr 11, 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 ancestral reconstruction of multiple-character indels under the PIP.
      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

    • STRs-in-CRC

      Public
      Notebooks and scripts for the analysis of short tandem repeat mutations in colorectal cancer data
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 16, 2023Oct 16, 2023

    • primate_SLC6A3

      Public
      Annotation of variable number tandem repeats (VNTRs) in primate SLC6A3 genes
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 2, 2023Oct 2, 2023