Repositories list

• ANNEVO

  Public
  Python

  •

  Other

  •1010 forks•118118 stars•99 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• STMiner

  Public
  bioinformatics-algorithmsspatial-transcriptomics

  bioinformatics-algorithmsspatial-transcriptomics

  Python

  •

  GNU General Public License v3.0

  •77 forks•1717 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• SpatialCOC

  Public
  We present SpatialCOC, a deep learning framework that deciphers cellular spatial organization and cross-omics relationships.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•55 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• MEIsensor

  Public
  MEIsensor, a deep-learning method for mobile element insertion discovery

  Python

  •11 fork•11 star•00 issues•00 pull requests•Updated Mar 21, 2026Mar 21, 2026

• HiArch

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

  Python

  •

  MIT License

  •11 fork•44 stars•11 issue•00 pull requests•Updated Feb 23, 2026Feb 23, 2026

• SpatialCOC_Old

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

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •11 fork•77 stars•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• LTR_Stream

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 24, 2025Jul 24, 2025

• HiCAT

  Public
  HiCAT new project

  Python

  •

  Other

  •44 forks•3434 stars•33 issues•00 pull requests•Updated May 18, 2025May 18, 2025

• Papaver-Genomics

  Public
  The genomic data for Papaver species

  Visual Basic 6.0

  •55 forks•33 stars•00 issues•00 pull requests•Updated May 18, 2025May 18, 2025

• BSLtool

  Public
  Build satellite library

  C++

  •22 forks•22 stars•00 issues•00 pull requests•Updated May 17, 2025May 17, 2025

• 2025-Kefaz-SValidation

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 9, 2025May 9, 2025

• 2025-SiqiJing-CBSVB

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•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+ 1

  deep-neural-networksstructral-variationsingle-molecule-sequencingcomplex-structural-variation

  Python

  •

  GNU General Public License v3.0

  •1212 forks•115115 stars•1818 issues•00 pull requests•Updated Apr 9, 2025Apr 9, 2025

• msisensor-pro

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

  next-generation-sequencinghypermutationmicrosatellite-instability+ 2

  next-generation-sequencinghypermutationmicrosatellite-instabilitydna-missmatch-repair-systemtumor-only-support

  C++

  •

  Other

  •2424 forks•116116 stars•77 issues•00 pull requests•Updated Apr 2, 2025Apr 2, 2025

• msisensor-rna

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

  rna-seqimmunotherapymicrosatellite-instability+ 1

  rna-seqimmunotherapymicrosatellite-instabilitydynamic-detection

  Python

  •

  Other

  •22 forks•2424 stars•55 issues•00 pull requests•Updated Feb 28, 2025Feb 28, 2025

• SVision-pro

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Dec 28, 2024Dec 28, 2024

• HiCAT-human

  Public
  HiCAT-human

  Python

  •

  Other

  •11 fork•00 stars•00 issues•00 pull requests•Updated Oct 31, 2024Oct 31, 2024

• cluster

  Public
  instruction of Ye-Lab HPC

  11 fork•11 star•00 issues•00 pull requests•Updated Sep 24, 2024Sep 24, 2024

• ChineseQuartetGenome

  Public
  Genome assembly and variant benchmarks for Chinese Quartet

  snvgenome-assemblystructural-variants+ 4

  snvgenome-assemblystructural-variantsindelchinese-quartetvariant-benchmarkhaplotype-resolved-assembly

  Python

  •

  MIT License

  •00 forks•55 stars•00 issues•00 pull requests•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

  •11 fork•00 stars•11 issue•00 pull requests•Updated Mar 28, 2024Mar 28, 2024

• processDrimm

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

  C#

  •11 fork•44 stars•00 issues•00 pull requests•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 resolut…

  C

  •

  GNU General Public License v3.0

  •9292 forks•33 stars•00 issues•00 pull requests•Updated Feb 28, 2024Feb 28, 2024

• Cross_landscape_HOR_clustering

  Public
  Init

  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 26, 2024Jan 26, 2024

• Four_Papaver_HiFi

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

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 28, 2023Oct 28, 2023

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

  Public
  2023, graduated student, YuXu's work

  22 forks•00 stars•00 issues•00 pull requests•Updated May 25, 2023May 25, 2023

• 2023-YuXu-poppy_subgenome

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

  22 forks•00 stars•00 issues•00 pull requests•Updated Aug 15, 2022Aug 15, 2022

• D2

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

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 20, 2022Jun 20, 2022

• IAGS

  Public
  Python

  •77 forks•1919 stars•77 issues•00 pull requests•Updated Apr 24, 2022Apr 24, 2022

• MCscanX2Band

  Public
  Java

  •

  MIT License

  •11 fork•22 stars•00 issues•00 pull requests•Updated Apr 21, 2022Apr 21, 2022

• IAG

  Public
  Python

  •44 forks•44 stars•00 issues•00 pull requests•Updated Feb 16, 2022Feb 16, 2022