Repositories list

• STMiner

  Public
  bioinformatics-algorithmsspatial-transcriptomics

  Python

  •

  GNU General Public License v3.0

  •7•15•0•0•Updated Aug 14, 2025Aug 14, 2025

• ANNEVO

  Public
  Python

  •

  GNU General Public License v3.0

  •1•24•7•0•Updated Aug 8, 2025Aug 8, 2025

• LTR_Stream

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •0•2•0•0•Updated Jul 24, 2025Jul 24, 2025

• HiCAT

  Public
  HiCAT new project

  Python

  •

  Other

  •4•28•2•0•Updated May 18, 2025May 18, 2025

• Papaver-Genomics

  Public
  The genomic data for Papaver species

  Visual Basic 6.0

  •5•3•0•0•Updated May 18, 2025May 18, 2025

• BSLtool

  Public
  Build satellite library

  C++

  •2•0•0•0•Updated May 17, 2025May 17, 2025

• SpatialCOC

  Public
  SpaKnit is a multimodal integration framework for spatial multi-omics data.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•6•0•0•Updated May 10, 2025May 10, 2025

• 2025-Kefaz-SValidation

  Public
  Python

  •0•0•0•0•Updated May 9, 2025May 9, 2025

• 2025-SiqiJing-CBSVB

  Public
  Python

  •0•0•0•0•Updated May 9, 2025May 9, 2025

• SVision

  Public
  Detecting genome structural variants with deep learning in single molecule sequencing

  deep-neural-networksstructral-variationsingle-molecule-sequencing+ 1complex-structural-variation

  Python

  •

  GNU General Public License v3.0

  •10•112•18•0•Updated Apr 9, 2025Apr 9, 2025

• msisensor-pro

  Public
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.

  next-generation-sequencinghypermutationmicrosatellite-instability+ 2dna-missmatch-repair-systemtumor-only-support

  C++

  •

  Other

  •24•110•4•0•Updated Apr 2, 2025Apr 2, 2025

• HiArch

  Public
  Measuring the high-order genome architectures (global folding and checkerboard) from Hi-C experiment

  Python

  •

  MIT License

  •1•1•1•0•Updated Mar 31, 2025Mar 31, 2025

• msisensor-rna

  Public
  MSIsensor-RNA: Microsatellite instability detection using RNA sequencing data

  immunotherapymicrosatellite-instabilitydynamic-detection+ 1rna-seq

  Python

  •

  Other

  •2•22•5•0•Updated Feb 28, 2025Feb 28, 2025

• SVision-pro

  Public
  0•0•0•0•Updated Dec 28, 2024Dec 28, 2024

• HiCAT-human

  Public
  HiCAT-human

  Python

  •

  Other

  •1•0•0•0•Updated Oct 31, 2024Oct 31, 2024

• cluster

  Public
  instruction of Ye-Lab HPC

  1•1•0•0•Updated Sep 24, 2024Sep 24, 2024

• ChineseQuartetGenome

  Public
  Genome assembly and variant benchmarks for Chinese Quartet

  snvgenome-assemblystructural-variants+ 4indelchinese-quartetvariant-benchmarkhaplotype-resolved-assembly

  Python

  •

  MIT License

  •0•3•0•0•Updated Jun 20, 2024Jun 20, 2024

• IAGS_AUTO

  Public
  The project is based on IAGS and automates processes

  Python

  •

  GNU General Public License v3.0

  •1•0•1•0•Updated Mar 28, 2024Mar 28, 2024

• processDrimm

  Public
  The input file generator for [IAGS](https://github.com/xjtu-omics/IAGS)

  C#

  •1•4•0•0•Updated Mar 26, 2024Mar 26, 2024

• pindel

  Public
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

  C

  •

  GNU General Public License v3.0

  •91•3•0•0•Updated Feb 28, 2024Feb 28, 2024

• Cross_landscape_HOR_clustering

  Public
  Init

  Python

  •1•0•0•0•Updated Jan 26, 2024Jan 26, 2024

• Four_Papaver_HiFi

  Public
  The analysis scripts used in four Papaver HiFi data analysis projects

  Python

  •0•0•0•0•Updated Oct 28, 2023Oct 28, 2023

• 2023-YuXu-Chromatin-accessibility-landscape-of-Papaver-somniferum_bak

  Public
  2023, graduated student, YuXu's work

  2•0•0•0•Updated May 25, 2023May 25, 2023

• 2023-YuXu-poppy_subgenome

  Public
  2023, graduated student, YuXu's work about poppy subgenome

  2•0•0•0•Updated Aug 15, 2022Aug 15, 2022

• D2

  Public
  D2: Compute DNA Density and Distance to nuclear periphery.

  Python

  •0•0•0•0•Updated Jun 20, 2022Jun 20, 2022

• IAGS

  Public
  Python

  •7•20•7•0•Updated Apr 24, 2022Apr 24, 2022

• MCscanX2Band

  Public
  Java

  •

  MIT License

  •1•2•0•0•Updated Apr 21, 2022Apr 21, 2022

• IAG

  Public
  Python

  •4•4•0•0•Updated Feb 16, 2022Feb 16, 2022

• opium_poppy_isoseq

  Public
  Python

  •0•0•0•0•Updated Sep 16, 2021Sep 16, 2021

• ArabidopsisAssem

  Public
  Arabidopsis thaliana high-quality genome assembly

  0•1•0•0•Updated Aug 13, 2021Aug 13, 2021