FertigLab

All

82 repositories

spatial-test
Public
Python
•0•0•0•0•Updated Nov 8, 2025Nov 8, 2025
fertiglab.github.io
Public
SCSS
•1•0•1•0•Updated Oct 19, 2025Oct 19, 2025
CoGAPS
Public
Bayesian MCMC matrix factorization algorithm
machine-learning bioinformatics bayesian-inference single-cell-rna-seq non-negative-matrix-factorization human-cell-atlas
C++
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BSD 3-Clause "New" or "Revised" License
•16•70•24•1•Updated Sep 19, 2025Sep 19, 2025
dpt-combined-analysis
Public
Jupyter Notebook
•0•0•0•0•Updated Sep 11, 2025Sep 11, 2025
Spatial_Venous_Invasion_PDAC
Public
Spatial profiling of venous invasion in human pancreatic ductal adenocarcinoma
HTML
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GNU General Public License v3.0
•0•0•0•0•Updated Aug 19, 2025Aug 19, 2025
Differential_Cell_Signaling_Test
Public
R
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GNU General Public License v3.0
•0•0•0•0•Updated Jul 7, 2025Jul 7, 2025
btc-spatial-pipelines
Public
Nextflow spatial pipelines (for Spatial Transcriptomics, IMC, etc.)
Nextflow
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MIT License
•1•0•0•0•Updated Jun 30, 2025Jun 30, 2025
pycogaps
Public
python API to the CoGAPS NMF package
Python
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GNU General Public License v2.0
•6•19•21•1•Updated May 19, 2025May 19, 2025
Homolig
Public
Homolig is a series of tools designed to compare the physiotypic properties of TCR and BCRs. Created by Alexander Girgis, Emily Davis-Marcisak, and Theron Palmer.
C++
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GNU Affero General Public License v3.0
•1•0•1•1•Updated May 12, 2025May 12, 2025
Human_PanIN_Spatial_Analysis
Public
R
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GNU General Public License v3.0
•0•0•0•0•Updated May 7, 2025May 7, 2025
J1798_trial_paper
Public
scripts for the J1798 trial paper
HTML
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MIT License
•0•0•0•0•Updated Mar 19, 2025Mar 19, 2025
J15221_trial_paper
Public
HTML
•0•0•0•0•Updated Mar 19, 2025Mar 19, 2025
dpt-visium-notebook
Public
Nextflow
•0•0•0•0•Updated Mar 10, 2025Mar 10, 2025
onboarding
Public
Ruby
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MIT License
•0•0•0•0•Updated Feb 10, 2025Feb 10, 2025
dominoSignal
Public
A software package for connecting cell level features in single cell RNA sequencing data with receptor ligand activity.
R
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GNU General Public License v3.0
•7•6•5•4•Updated Feb 10, 2025Feb 10, 2025
bayestme
Public
BayesTME: A reference-free Bayesian method for analyzing spatial transcriptomics data
Jupyter Notebook
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Other
•4•0•0•0•Updated Feb 4, 2025Feb 4, 2025
spatial-pipeline
Public
Nextflow
•0•0•7•0•Updated Nov 22, 2024Nov 22, 2024
HCCTLS
Public
R
•2•2•0•0•Updated Nov 15, 2024Nov 15, 2024
prgpmf
Public
Poisson-randomized gamma Poisson matrix factorization
Python
•3•0•0•0•Updated Nov 2, 2024Nov 2, 2024
ATACCoGAPS
Public
R
•1•4•0•0•Updated Oct 22, 2024Oct 22, 2024
actions
Public
R
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GNU General Public License v3.0
•0•0•1•0•Updated Aug 12, 2024Aug 12, 2024
splicemutr
Public
R
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GNU General Public License v3.0
•1•7•0•0•Updated Jul 5, 2024Jul 5, 2024
hypoxiaROSanalysis
Public
Python
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MIT License
•0•1•0•0•Updated Jul 3, 2024Jul 3, 2024
PanIN_carcinogeneisis_spatial_analysis
Public
HTML
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GNU General Public License v3.0
•1•0•1•0•Updated Jun 4, 2024Jun 4, 2024
mKRAS-Vax
Public
scRNA and TCR analysis, including T-cell expansion assays, from subjects in J1994 manuscript by Huff et al.
R
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GNU General Public License v3.0
•0•0•0•0•Updated May 20, 2024May 20, 2024
nf-bin-test
Public
Nextflow
•0•0•0•0•Updated May 16, 2024May 16, 2024
nfcore-modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
Nextflow
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MIT License
•938•0•0•0•Updated Apr 30, 2024Apr 30, 2024
GeneosCollaboration
Public
Repository for R code for single cell sequencing analysis published in Yarchoan, M., Gane, E.J., Marron, T.U. et al. Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial. Nat Med (2024).
R
•1•7•0•0•Updated Apr 8, 2024Apr 8, 2024
git-test
Public
0•0•3•1•Updated Mar 15, 2024Mar 15, 2024
PacVAX2_pancvaxICI_scRNAseq
Public
scRNAseq and survival analysis in Panc02-bearing mice treated with PancVAX and immune checkpoint inhibition
R
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GNU General Public License v3.0
•0•0•0•0•Updated Oct 12, 2023Oct 12, 2023