xjtu-omics

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51 repositories

ANNEVO
Public
Python
•
Other
•4•91•13•0•Updated Mar 20, 2026Mar 20, 2026
STMiner
Public
bioinformatics-algorithms spatial-transcriptomics
bioinformatics-algorithms spatial-transcriptomics
Python
•
GNU General Public License v3.0
•7•16•0•0•Updated Mar 11, 2026Mar 11, 2026
HiArch
Public
Measuring the high-order genome architectures (global folding and checkerboard) from Hi-C experiment
Python
•
MIT License
•1•2•0•0•Updated Feb 23, 2026Feb 23, 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
•0•2•0•0•Updated Feb 10, 2026Feb 10, 2026
SpatialCOC_Old
Public
SpatialCOC is a multimodal integration framework for spatial multi-omics data.
Jupyter Notebook
•
GNU General Public License v3.0
•1•7•0•0•Updated Feb 10, 2026Feb 10, 2026
LTR_Stream
Public
Python
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GNU Affero General Public License v3.0
•0•2•0•0•Updated Jul 24, 2025Jul 24, 2025
HiCAT
Public
HiCAT new project
Python
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Other
•4•34•3•0•Updated May 18, 2025May 18, 2025
Papaver-Genomics
Public
The genomic data for Papaver species
Visual Basic 6.0
•5•3•0•0•Updated May 18, 2025May 18, 2025
BSLtool
Public
Build satellite library
C++
•2•2•0•0•Updated May 17, 2025May 17, 2025
2025-Kefaz-SValidation
Public
Python
•0•0•0•0•Updated May 9, 2025May 9, 2025
2025-SiqiJing-CBSVB
Public
Python
•0•0•0•0•Updated May 9, 2025May 9, 2025
SVision
Public
Detecting genome structural variants with deep learning in single molecule sequencing
deep-neural-networks structral-variation single-molecule-sequencing
deep-neural-networks structral-variation single-molecule-sequencing complex-structural-variation
Python
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GNU General Public License v3.0
•12•115•18•0•Updated Apr 9, 2025Apr 9, 2025
msisensor-pro
Public
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
next-generation-sequencing hypermutation microsatellite-instability
next-generation-sequencing hypermutation microsatellite-instability dna-missmatch-repair-system tumor-only-support
C++
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Other
•24•115•6•0•Updated Apr 2, 2025Apr 2, 2025
msisensor-rna
Public
MSIsensor-RNA: Microsatellite instability detection using RNA sequencing data
rna-seq immunotherapy microsatellite-instability
rna-seq immunotherapy microsatellite-instability dynamic-detection
Python
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Other
•2•24•5•0•Updated Feb 28, 2025Feb 28, 2025
SVision-pro
Public
0•0•0•0•Updated Dec 28, 2024Dec 28, 2024
HiCAT-human
Public
HiCAT-human
Python
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Other
•1•0•0•0•Updated Oct 31, 2024Oct 31, 2024
cluster
Public
instruction of Ye-Lab HPC
1•1•0•0•Updated Sep 24, 2024Sep 24, 2024
ChineseQuartetGenome
Public
Genome assembly and variant benchmarks for Chinese Quartet
snv genome-assembly structural-variants
snv genome-assembly structural-variants indel chinese-quartet variant-benchmark haplotype-resolved-assembly
Python
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MIT License
•0•4•0•0•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
•1•0•1•0•Updated Mar 28, 2024Mar 28, 2024
processDrimm
Public
The input file generator for [IAGS](https://github.com/xjtu-omics/IAGS)
C#
•1•4•0•0•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
•92•3•0•0•Updated Feb 28, 2024Feb 28, 2024
Cross_landscape_HOR_clustering
Public
Init
Python
•1•0•0•0•Updated Jan 26, 2024Jan 26, 2024
Four_Papaver_HiFi
Public
The analysis scripts used in four Papaver HiFi data analysis projects
Python
•0•0•0•0•Updated Oct 28, 2023Oct 28, 2023
2023-YuXu-Chromatin-accessibility-landscape-of-Papaver-somniferum_bak
Public
2023, graduated student, YuXu's work
2•0•0•0•Updated May 25, 2023May 25, 2023
2023-YuXu-poppy_subgenome
Public
2023, graduated student, YuXu's work about poppy subgenome
2•0•0•0•Updated Aug 15, 2022Aug 15, 2022
D2
Public
D2: Compute DNA Density and Distance to nuclear periphery.
Python
•0•1•0•0•Updated Jun 20, 2022Jun 20, 2022
IAGS
Public
Python
•7•19•7•0•Updated Apr 24, 2022Apr 24, 2022
MCscanX2Band
Public
Java
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MIT License
•1•2•0•0•Updated Apr 21, 2022Apr 21, 2022
IAG
Public
Python
•4•4•0•0•Updated Feb 16, 2022Feb 16, 2022
opium_poppy_isoseq
Public
Python
•0•0•0•0•Updated Sep 16, 2021Sep 16, 2021