Yu Laboratory @ St. Jude

All

19 repositories

Spotiphy
Public
Spot pseudo-Imager on top of histology
Jupyter Notebook
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Apache License 2.0
•2•3•0•0•Updated Jan 24, 2025Jan 24, 2025
NetBID_shiny
Public
NetBID shiny app
R
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Apache License 2.0
•0•2•0•0•Updated Jan 20, 2025Jan 20, 2025
MICA
Public
Mutual Information-based Non-linear Clustering Analysis
dimensionality-reduction mutual-information single-cell-rna-seq graph-embedding clustering-analysis
Python
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Apache License 2.0
•3•2•2•2•Updated Jan 7, 2025Jan 7, 2025
redeconv
Public
Python
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Apache License 2.0
•1•6•2•0•Updated Jan 2, 2025Jan 2, 2025
NetBID
Public
Data-driven Network-based Bayesian Inference of Drivers
bayesian-inference r-package network-analysis rna-seq-analysis scrna-seq-analysis
R
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Apache License 2.0
•9•41•8•1•Updated Dec 21, 2024Dec 21, 2024
scMINER
Public
Single-cell Mutual Information-based Network Engineering Ranger
clustering mutual-information activity-map single-cell-rna-seq network-construction master-regulator
R
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Apache License 2.0
•3•9•2•0•Updated Nov 13, 2024Nov 13, 2024
scMINER_analysis
Public
Codes used for benchmarking scMINER in cell clustering, network inference and hidden driver identification
Jupyter Notebook
•0•0•0•0•Updated Oct 18, 2024Oct 18, 2024
scMINER_documentation
Public
This a the full documentation of scMINER R package.
TeX
•0•0•0•0•Updated Oct 5, 2024Oct 5, 2024
ScreenBEAM2
Public
Gene-level meta-analysis of high-throughput functional genomics (RNAi or CRISPR) screens.
R
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Apache License 2.0
•0•0•0•0•Updated Jul 25, 2024Jul 25, 2024
MICA-archive2
Public archive
Mutual Information-based Non-linear Clustering Analysis
Python
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Apache License 2.0
•3•0•0•0•Updated May 30, 2024May 30, 2024
MICA-archive
Public archive
Mutual Information-based Non-linear Clustering Analysis
Python
•
Apache License 2.0
•3•0•0•0•Updated May 30, 2024May 30, 2024
SJARACNe
Public
Scalable Tool for Gene Network Reverse Engineering
inference mutual-information gene-network
C++
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Other
•16•23•10•0•Updated May 28, 2024May 28, 2024
Asparaginase-Venetoclax-in-B-ALL
Public
Asparaginase-Venetoclax in B-ALL
R
•2•0•0•0•Updated May 27, 2024May 27, 2024
LVIS_pipeline
Public
Compile lentiviral vector integration sites from sequencing pipeline
gene-therapy vector-integration-sites lentivirus
Jupyter Notebook
•4•2•0•0•Updated Jul 14, 2023Jul 14, 2023
dasatinib-TALL
Public
dasatinib sensitivity biomarker in T-ALL
R
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Apache License 2.0
•2•1•1•0•Updated Mar 16, 2022Mar 16, 2022
Heptoblastoma_Cxcl1
Public
0•0•0•0•Updated Oct 19, 2021Oct 19, 2021
CMPB-Practicum
Public
Computational Biology Practicum Materials
Jupyter Notebook
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Apache License 2.0
•0•0•0•0•Updated Aug 22, 2020Aug 22, 2020
HDAC6-score
Public
Network-based assessment of HDAC6 activity is highly predictive of pre-clinical and clinical response to the HDAC6 inhibitor
R
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Apache License 2.0
•2•3•0•0•Updated Apr 21, 2020Apr 21, 2020
ScreenBEAM
Public
Gene-level meta-analysis of high-throughput functional genomics (RNAi or CRISPR) screens.
R
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MIT License
•8•0•0•0•Updated Jul 19, 2016Jul 19, 2016