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@acg-team Applied Computational Genomics Team

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    38 repositories

    • ConSTRain

      Public
      A short tandem repeat variant caller that incorporates copy number information
      Rust
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 27, 2024Dec 27, 2024

    • multicancer_STR

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • rust-phylo

      Public
      Phylo library in Rust
      Rust
      •
      MIT License
      •2•3•0•0•Updated Dec 18, 2024Dec 18, 2024

    • 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 Dec 10, 2024Dec 10, 2024

    • 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

    • 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•5•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

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jun 7, 2024Jun 7, 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
      •1•1•1•0•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

    • bpp-arpip

      Public
      ARPIP: Ancestral sequence Reconstruction under PIP
      ancestral-sequence-reconstruction
      C++
      •1•9•1•0•Updated Oct 2, 2023Oct 2, 2023

    • JATI

      Public
      Initial attempt at JATI in Rust
      Rust
      •0•0•0•0•Updated Aug 11, 2023Aug 11, 2023

    • tral

      Public
      Tandem Repeat Annotation Library
      Python
      •
      GNU General Public License v2.0
      •7•24•8•1•Updated Mar 30, 2023Mar 30, 2023

    • MEDOBO

      Public
      Python
      •0•1•0•0•Updated Jun 7, 2022Jun 7, 2022

    • LBD-Demo

      Public
      0•0•0•0•Updated Feb 23, 2022Feb 23, 2022

    • Relation-Extraction

      Public
      Python
      •0•0•0•0•Updated Dec 25, 2021Dec 25, 2021

    • ProPIP

      Public
      C++
      •
      GNU Lesser General Public License v3.0
      •3•6•3•0•Updated Aug 4, 2021Aug 4, 2021

    • swissprot_human_strs

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 22, 2021Mar 22, 2021

    • twins_microbiome_pipeline

      Public
      Bioinformatics processing of raw Illumina reads for microbiome analysis of twins (dada2)
      R
      •1•1•0•0•Updated Jan 11, 2021Jan 11, 2021

    • ProGraphMSA

      Public
      ProGraphMSA is a state-of-the-art multiple sequence alignment tool which produces phylogenetically sensible gap patterns while maintaining robustness by allowing alternative splicings and errors in the branching pattern of the guide tree. Fork of ProGraphMSA+TR from https://sourceforge.net/projects/prographmsa
      C++
      •
      GNU General Public License v3.0
      •4•9•2•0•Updated Sep 29, 2020Sep 29, 2020

    • STFT-matlab

      Public
      MATLAB
      •0•1•0•0•Updated Sep 3, 2020Sep 3, 2020

    • swissrepeats

      Public
      Delucchi, M.; Schaper, E.; Sachenkova, O.; Elofsson, A.; Anisimova, M. A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder. Genes 2020, 11, 407.
      HTML
      •
      MIT License
      •1•1•0•0•Updated May 25, 2020May 25, 2020

    • TRAL-Result-Analysis

      Public
      R package to get the most out of the results from TRAL
      R
      •
      Creative Commons Attribution Share Alike 4.0 International
      •1•0•0•0•Updated Jun 29, 2019Jun 29, 2019