DeepOmics Lab

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62 repositories

TCREmbedding
Public
Python
•
MIT License
•2•1•0•0•Updated Feb 1, 2025Feb 1, 2025
StrInt
Public
Python
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MIT License
•0•0•0•0•Updated Jan 26, 2025Jan 26, 2025
mrnadesign_web
Public
Vue
•0•0•0•0•Updated Jan 24, 2025Jan 24, 2025
mrnadesign_api
Public
Jupyter Notebook
•0•0•0•0•Updated Jan 24, 2025Jan 24, 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 Jan 24, 2025Jan 24, 2025
TCRsep
Public
Python
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MIT License
•0•0•0•0•Updated Jan 23, 2025Jan 23, 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
CASCAT
Public
Jupyter Notebook
•0•1•0•0•Updated Jan 17, 2025Jan 17, 2025
Genome-wide-coverage-profiling
Public
Jupyter Notebook
•0•0•0•0•Updated Jan 9, 2025Jan 9, 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
•1•3•0•0•Updated Dec 12, 2024Dec 12, 2024
DeepHost
Public
This is the repository for DeepHost, a phage host prediction tool.
Python
•0•19•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
•7•39•1•0•Updated Dec 12, 2024Dec 12, 2024
CeiTEA
Public
Julia
•0•0•0•0•Updated Dec 9, 2024Dec 9, 2024
SPIDER
Public
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Dec 5, 2024Dec 5, 2024
CERNATAX
Public
Detecting ceRNA network mRNA-miRNA-lncRNA triplet axis
Python
•0•1•0•0•Updated Nov 23, 2024Nov 23, 2024
TCRclub
Public
Jupyter Notebook
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MIT License
•0•0•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
STAGUE
Public
Jupyter Notebook
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MIT License
•0•2•0•0•Updated Oct 22, 2024Oct 22, 2024
AlphaTalk
Public
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Oct 21, 2024Oct 21, 2024
crustdb_web
Public
Vue
•0•0•0•0•Updated Oct 11, 2024Oct 11, 2024
crustdb_api
Public
Jupyter Notebook
•0•0•0•0•Updated Oct 11, 2024Oct 11, 2024
GutMeta_analysis_scripts
Public
Python
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GNU General Public License v3.0
•1•0•0•0•Updated Oct 8, 2024Oct 8, 2024
plasmid_web
Public
Vue
•0•0•0•0•Updated Oct 1, 2024Oct 1, 2024
plasmid_api
Public
Python
•0•0•0•0•Updated Sep 29, 2024Sep 29, 2024
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•40•10•0•Updated Sep 25, 2024Sep 25, 2024
LocalHGT
Public
Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.
metagenomics microbiome hgt k-mer strain bacterial-genome-analysis horizental-gene-transfer structual-variation mobile-gene-element
Python
•1•13•1•0•Updated Aug 8, 2024Aug 8, 2024