Repositories list

• MicrobialScope-API

  Public
  Python

  •0•0•0•0•Updated Jul 19, 2025Jul 19, 2025

• 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 and amplicon data. It supports PacBio and Nanopore data.

  nanoporetgspacbio+ 10tcrighla-typingimmunebcrlong-read-sequencingvdj+ 3

  F*

  •

  MIT License

  •0•24•1•0•Updated Jul 18, 2025Jul 18, 2025

• MicrobialScope-WEB

  Public
  JavaScript

  •0•0•0•0•Updated Jul 18, 2025Jul 18, 2025

• CoMBCR

  Public
  Jupyter Notebook

  •

  Other

  •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

• mrnadesign_web

  Public
  Vue

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

• mrnadesign_api

  Public
  Jupyter Notebook

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

• crustdb_web

  Public
  Vue

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

• crustdb_api

  Public
  Jupyter Notebook

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

• EAMHCDOC

  Public
  0•0•0•0•Updated Jun 28, 2025Jun 28, 2025

• SPOKE

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

  Python

  •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

• TCRsep

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 16, 2025Jun 16, 2025

• CASCAT

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Jun 13, 2025Jun 13, 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

• INVAS

  Public
  rna-seqassemblyngs+ 4cancer-genomicsoncogenomicsrna-assemblyintragenic-inversion

  Python

  •0•1•0•0•Updated Jun 4, 2025Jun 4, 2025

• StrInt

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated May 8, 2025May 8, 2025

• PALACE

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

  C

  •

  MIT License

  •1•1•0•0•Updated May 1, 2025May 1, 2025

• OmicsSankey

  Public
  Jupyter Notebook

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

• CeiTEA

  Public
  Julia

  •0•0•0•0•Updated Apr 9, 2025Apr 9, 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, it supports both short- and long-read data.

  nanoporecancerphase+ 12immunityhla-typingpacbio-datalocal-assemblylohhaplotypereads-binning+ 5

  C++

  •

  MIT License

  •11•46•7•0•Updated Mar 28, 2025Mar 28, 2025

• HGT_network

  Public
  Network analysis for hgt network (plasmid)

  Jupyter Notebook

  •0•0•0•0•Updated Mar 21, 2025Mar 21, 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+ 4partial-information-decompositionmicrobial-interactionshuman-gutfunctional-redundancy

  Python

  •

  MIT License

  •0•2•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+ 2single-cell-multiomicssingle-cell-multi-omics

  Python

  •

  MIT License

  •0•3•0•0•Updated Dec 12, 2024Dec 12, 2024

• DeepHost

  Public
  This is the repository for DeepHost, a phage host prediction tool.

  Python

  •0•20•0•0•Updated Dec 12, 2024Dec 12, 2024

• SeCNV

  Public
  This is the repository for SeCNV, a single cell copy number profiling tool.

  Python

  •2•10•3•0•Updated Dec 12, 2024Dec 12, 2024

• Graphage

  Public
  This is the repository for GraphPhage, a phage analysis tool that integrates phage and ICE discrimination, phage integration site prediction, phage lifestyle prediction, and phage host prediction.

  phagephage-bacteria-networksphage-genomes+ 3phage-host-predictionphage-annotationphage-activity

  Python

  •1•9•0•0•Updated Dec 12, 2024Dec 12, 2024

• GCNFrame

  Public
  This is a python package for genomics study with a GCN framework.

  genomeembeddinggcn

  Python

  •

  MIT License

  •8•41•2•1•Updated Dec 12, 2024Dec 12, 2024

• SPIDER

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

• TCRclub

  Public
  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Nov 20, 2024Nov 20, 2024