DeepOmics Lab

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68 repositories

MicrobialScope-API
Public
Python
•0•0•0•0•Updated Jun 18, 2025Jun 18, 2025
MicrobialScope-WEB
Public
JavaScript
•0•0•0•0•Updated Jun 18, 2025Jun 18, 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
CoMBCR
Public
Jupyter Notebook
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Other
•0•0•0•0•Updated Jun 17, 2025Jun 17, 2025
TCRsep
Public
Python
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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
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GNU General Public License v3.0
•0•0•0•0•Updated Jun 13, 2025Jun 13, 2025
mrnadesign_api
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 10, 2025Jun 10, 2025
INVAS
Public
rna-seq assembly ngs cancer-genomics oncogenomics rna-assembly intragenic-inversion
Python
•0•1•0•0•Updated Jun 4, 2025Jun 4, 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.
nanopore tgs pacbio tcr ig hla-typing immune bcr long-read-sequencing vdj
F*
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MIT License
•0•22•2•0•Updated May 18, 2025May 18, 2025
StrInt
Public
Jupyter Notebook
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MIT License
•0•0•0•0•Updated May 8, 2025May 8, 2025
PALACE
Public
A tool to assemble high-quality phages from metagenomes.
C
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MIT License
•1•1•0•0•Updated May 1, 2025May 1, 2025
mrnadesign_web
Public
Vue
•0•0•0•0•Updated Apr 23, 2025Apr 23, 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.
nanopore cancer phase immunity hla-typing pacbio-data local-assembly loh haplotype reads-binning
C++
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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
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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-communities metagenomic-analysis gut-microbiome partial-information-decomposition microbial-interactions human-gut functional-redundancy
Python
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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-cell tensor-decomposition single-cell-omics single-cell-multiomics single-cell-multi-omics
Python
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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.
phage phage-bacteria-networks phage-genomes phage-host-prediction phage-annotation phage-activity
Python
•1•8•0•0•Updated Dec 12, 2024Dec 12, 2024
GCNFrame
Public
This is a python package for genomics study with a GCN framework.
genome embedding gcn
Python
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MIT License
•8•41•2•1•Updated Dec 12, 2024Dec 12, 2024
SPIDER
Public
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Dec 5, 2024Dec 5, 2024
TCRclub
Public
Jupyter Notebook
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MIT License
•0•1•0•0•Updated Nov 20, 2024Nov 20, 2024
FR_Hierarchy_Gut
Public
Jupyter Notebook
•0•0•0•0•Updated Nov 6, 2024Nov 6, 2024
SPIDER-paper
Public
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Oct 30, 2024Oct 30, 2024
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 within its framework.
Python
•0•0•0•0•Updated Oct 25, 2024Oct 25, 2024