Repositories list

• rust-phylo

  Public
  Phylo library in Rust

  Rust

  •

  MIT License

  •2•6•7•3•Updated Feb 26, 2025Feb 26, 2025

• JATI

  Public
  JATI: Joint Alignment and Tree Inference

  Rust

  •0•1•0•1•Updated Feb 23, 2025Feb 23, 2025

• Bioinfo4B

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Feb 19, 2025Feb 19, 2025

• tmb_crc_scripts

  Public
  0•0•0•0•Updated Feb 18, 2025Feb 18, 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 Feb 11, 2025Feb 11, 2025

• crc_ml_genotype

  Public
  Machine learning analysis of genotype-phenotype associations in colorectal cancer using tumor images and mutation data from TCGA.

  0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• images_tcga

  Public
  0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

• 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 Jan 13, 2025Jan 13, 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

• multicancer_STR

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• nf-core-pvacseq

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Dec 2, 2024Dec 2, 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

• 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)

  apibioinformaticsgenomics+ 1tandem-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

  visualizationpythonphylogeny+ 1ancestral-state-reconstruction

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Nov 9, 2023Nov 9, 2023

• indelMaP

  Public
  Python

  •1•3•0•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

• tral

  Public
  Tandem Repeat Annotation Library

  Python

  •

  GNU General Public License v2.0

  •6•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