Crawford Lab

All

18 repositories

mmer
Public
A computationally efficient method which detects statistical epistasis in complex traits.
genetics epistasis
C++
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Other
•0•0•0•0•Updated Dec 15, 2024Dec 15, 2024
Geneformer
Public
Python
•0•0•0•0•Updated Dec 14, 2024Dec 14, 2024
cancer-drug-synergy-prediction
Public
Github repo for cancer drug synergy prediction work
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Dec 10, 2024Dec 10, 2024
recall
Public
Calibrated clustering with artificial variables to avoid over-clustering in single-cell RNA-sequencing
clustering single-cell single-cell-genomics single-cell-rna-seq single-cell-analysis knockoffs knockoff-filter
R
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Other
•0•0•0•0•Updated Nov 19, 2024Nov 19, 2024
mvMAPIT
Public
The multivariate MArginal ePIstasis Test
gwas cpp linear-mixed-models epistasis variance-components epistasis-analysis gwas-tools mapit mvmapit cran
R
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GNU General Public License v3.0
•1•11•0•0•Updated Oct 21, 2024Oct 21, 2024
callback
Public
Calibrated clustering via knockoffs for single-cell genomics
clustering single-cell single-cell-genomics single-cell-rna-seq knockoffs
R
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Other
•0•10•0•0•Updated Jul 11, 2024Jul 11, 2024
i-LDSC
Public
Code and simulations using interaction-LD score regression
gwas epistasis heritability gwas-tools gwas-summary-statistics ld-score-regression heritability-estimation
Python
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GNU General Public License v3.0
•1•13•1•0•Updated Jul 2, 2024Jul 2, 2024
multio-viz
Public
A platform for the interactive assessment of gene regulatory networks
bioinformatics genomics genetics gene-regulatory-network in-silico-perturbation
R
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GNU General Public License v3.0
•0•3•0•0•Updated May 10, 2024May 10, 2024
SINATRA-Pro
Public
Topological data analytic approach for discovering biophysical signatures in protein dynamics
protein-structure variable-selection topological-data-analysis protein-dynamics 3d-shapes protein-analysis centrality-measures euler-characteristics
Python
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MIT License
•0•4•0•0•Updated Mar 14, 2024Mar 14, 2024
callbackreproducibility
Public
R
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Other
•0•0•0•0•Updated Mar 13, 2024Mar 13, 2024
ashapesampler_paper_results
Public
Code to reproduce analyses and results provided in the alpha shape sampler paper beyond what is given in the R package.
HTML
•0•0•0•0•Updated Feb 1, 2024Feb 1, 2024
ashapesampler
Public
R package for generating synthetic shapes and images using the α-shape sampler
shape image-generation r-package topological-data-analysis 2d-images 3d-shapes alpha-shapes shape-generation
R
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GNU General Public License v3.0
•1•0•0•0•Updated Feb 1, 2024Feb 1, 2024
GOALS
Public
Code and tutorials for implementing the GlObal And Local Score
machine-learning genetics variable-importance variable-selection gp-regression nonlinear-models
R
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GNU Affero General Public License v3.0
•0•0•0•0•Updated Oct 20, 2023Oct 20, 2023
SINATRA
Public
A statistical framework for feature selection and association mapping with 3D shapes
r variable-selection r-package nonparametric-regression 3d-reconstruction topological-data-analysis shape-reconstruction shape-analysis 3d-shapes centrality-measures
R
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GNU General Public License v3.0
•4•8•0•0•Updated Sep 9, 2023Sep 9, 2023
SINATRA_Pro_Paper_Results
Public
Reproducibility repo for the simulation and real data results in the SINATRA Pro manuscript
Python
•0•0•0•0•Updated Mar 23, 2023Mar 23, 2023
ltsim
Public
A liability threshold linear mixed model simulation tool for case-control studies.
R
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GNU General Public License v2.0
•0•0•0•0•Updated Feb 9, 2023Feb 9, 2023
SINATRA_AoAS_Results
Public
Reproducibility repo for the simulation and real data results in the SINATRA manuscript set to appear in AoAS.
variable-selection nonparametric-regression 3d-reconstruction topological-data-analysis shape-reconstruction shape-analysis 3d-shapes
HTML
•0•0•0•0•Updated Nov 15, 2022Nov 15, 2022
BANNs
Public
Code and simulations using biologically annotated neural networks
machine-learning gwas genetics variable-selection neural-networks bayesian-statistics interpretability gwas-tools
HTML
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GNU General Public License v3.0
•3•21•1•0•Updated Aug 23, 2021Aug 23, 2021