Repositories list

• MetaTCR_exp_scripts

  Public
  Contains the scripts used to generate the figures and results for the paper MetaTCR

  Python

  •0•0•0•0•Updated Feb 25, 2026Feb 25, 2026

• SpecImmune

  Public
  Accurate Typing of Diverse Immune-Related Gene Families from Long-Read Sequencing Data. It can handle HLA, KIR, IG, TCR, CYP gene families. It supports both WGS…

  nanoporetgspacbio+ 10

  nanoporetgspacbiotcrighla-typingimmunebcrlong-read-sequencingvdj+ 3

  F*

  •

  MIT License

  •1•33•0•0•Updated Feb 19, 2026Feb 19, 2026

• MetaTCR

  Public
  Python

  •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

• LocalHGT

  Public
  Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.

  metagenomicsmicrobiomehgt+ 6

  metagenomicsmicrobiomehgtk-merstrainbacterial-genome-analysishorizental-gene-transferstructual-variationmobile-gene-element

  Python

  •1•19•1•0•Updated Feb 2, 2026Feb 2, 2026

• mrnadesign_web

  Public
  Vue

  •1•0•0•0•Updated Jan 30, 2026Jan 30, 2026

• mrnadesign_api

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Jan 29, 2026Jan 29, 2026

• CoMBCR

  Public
  Jupyter Notebook

  •

  Other

  •0•0•0•0•Updated Jan 28, 2026Jan 28, 2026

• DeepTAPE-1.0

  Public
  DeepTAPE is an advanced deep learning tool designed to provide reference diagnostics for SLE, leveraging pre-trained models and supporting custom training withi…

  Python

  •0•1•0•1•Updated Jan 16, 2026Jan 16, 2026

• EAMHCDOC

  Public
  0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

• PALACE

  Public
  A tool to assemble high-quality phages from metagenomes.

  Python

  •

  MIT License

  •1•1•0•0•Updated Dec 24, 2025Dec 24, 2025

• INVAS

  Public
  rna-seqassemblyngs+ 4

  rna-seqassemblyngscancer-genomicsoncogenomicsrna-assemblyintragenic-inversion

  Python

  •0•1•0•0•Updated Dec 14, 2025Dec 14, 2025

• MicrobialScope-WEB

  Public
  JavaScript

  •0•0•0•0•Updated Nov 23, 2025Nov 23, 2025

• GeneFamily_Database

  Public
  Python

  •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

• MicrobialScope-API

  Public
  Python

  •0•0•0•0•Updated Oct 15, 2025Oct 15, 2025

• CASCAT

  Public
  Jupyter Notebook

  •0•3•1•0•Updated Oct 14, 2025Oct 14, 2025

• SpecHLA

  Public
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, …

  nanoporecancerphase+ 12

  nanoporecancerphaseimmunityhla-typingpacbio-datalocal-assemblylohhaplotypereads-binning+ 5

  C++

  •

  MIT License

  •14•56•10•0•Updated Oct 9, 2025Oct 9, 2025

• FR_Hierarchy_Gut

  Public
  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Sep 27, 2025Sep 27, 2025

• TCRsep

  Public
  Python

  •

  MIT License

  •0•4•0•0•Updated Aug 21, 2025Aug 21, 2025

• StrInt

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

• SPOKE

  Public
  A tool for analyzing how cells spatially SPOKE to each other.

  Python

  •0•0•0•0•Updated Aug 2, 2025Aug 2, 2025

• HGT_network

  Public
  Network analysis for hgt network (plasmid)

  Jupyter Notebook

  •0•0•0•0•Updated Jul 27, 2025Jul 27, 2025

• crustdb_web

  Public
  Vue

  •1•0•0•0•Updated Jul 7, 2025Jul 7, 2025

• crustdb_api

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Jul 7, 2025Jul 7, 2025

• AffMB

  Public
  AffMB: affinity maturation of B-cell receptors

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 13, 2025Jun 13, 2025

• OmicsSankey

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Apr 14, 2025Apr 14, 2025

• CeiTEA

  Public
  Julia

  •0•0•0•0•Updated Apr 9, 2025Apr 9, 2025

• Genome-wide-coverage-profiling

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 15, 2025Feb 15, 2025

• TCREmbedding

  Public
  Python

  •

  MIT License

  •3•2•0•0•Updated Feb 12, 2025Feb 12, 2025

• Interaction-redundancy

  Public
  Deciphering microbial interactions with functional redundancy in human microbial community with partial information decomposition.

  microbial-communitiesmetagenomic-analysisgut-microbiome+ 4

  microbial-communitiesmetagenomic-analysisgut-microbiomepartial-information-decompositionmicrobial-interactionshuman-gutfunctional-redundancy

  Python

  •

  MIT License

  •0•3•0•0•Updated Jan 18, 2025Jan 18, 2025

• SCOIT

  Public
  SCOIT is an implementation of a probabilistic tensor decomposition framework for single-cell multi-omics data integration.

  single-celltensor-decompositionsingle-cell-omics+ 2

  single-celltensor-decompositionsingle-cell-omicssingle-cell-multiomicssingle-cell-multi-omics

  Python

  •

  MIT License

  •2•5•0•0•Updated Dec 12, 2024Dec 12, 2024