Caravagna Lab

All

36 repositories

DeConveil
Public
Extension of Differential Gene Expression testing to handle genome aneuploidy in cancer
Jupyter Notebook
•1•0•0•0•Updated Feb 7, 2025Feb 7, 2025
rRACES-examples
Public
HTML
•0•0•1•0•Updated Feb 7, 2025Feb 7, 2025
tickTack
Public
Timing Inference for Copy number alterations: Tracking Alterations in Cancer Karyotypes
R
•
Other
•0•0•0•0•Updated Jan 31, 2025Jan 31, 2025
pylineaGT
Public
A Pyro model to perform lineage inference from Gene Therapy assays
Jupyter Notebook
•
GNU General Public License v3.0
•0•1•0•0•Updated Jan 31, 2025Jan 31, 2025
lineaGT
Public
Lineage inference from Gene Therapy assays with insertional mutagenesis and somatic mutations
somatic-mutations clonal-evolution gene-therapy lineage-tracing
R
•
GNU General Public License v3.0
•0•1•0•0•Updated Jan 31, 2025Jan 31, 2025
tumourevo
Public
Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
GNU General Public License v3.0
•5•0•0•0•Updated Jan 30, 2025Jan 30, 2025
rRACES
Public
R wrapper for the RACES package
C++
•
GNU General Public License v3.0
•1•2•8•0•Updated Jan 15, 2025Jan 15, 2025
mobster
Public
Model-based subclonal deconvolution from bulk sequencing.
mixture-model pareto-distributions beta-distribution model-based-clustering subclone-identification
HTML
•
GNU General Public License v3.0
•8•33•2•0•Updated Dec 30, 2024Dec 30, 2024
devil
Public
devil
C++
•
Other
•1•2•0•0•Updated Dec 10, 2024Dec 10, 2024
biPOD
Public
Bayesian inference for population dynamics
population-dynamics
R
•
GNU General Public License v3.0
•0•0•0•0•Updated Nov 28, 2024Nov 28, 2024
INCOMMON
Public
Inference of copy number and mutation multiplicity in oncology
cancer-genomics survival-analysis bayesian-inference copy-number-variation biomarker-discovery metastasis
R
•
Other
•1•1•0•0•Updated Nov 22, 2024Nov 22, 2024
CONGASp
Public
Python
•
GNU General Public License v3.0
•0•4•1•0•Updated Nov 20, 2024Nov 20, 2024
bascule
Public
Detecting mutational signatures via bayesian inference and a reference catalog
genomics cancer variational-inference cosmic non-negative-matrix-factorization mutational-signatures
R
•
GNU General Public License v3.0
•1•1•1•0•Updated Nov 8, 2024Nov 8, 2024
rcongas
Public
rcongas
R
•
GNU General Public License v3.0
•1•7•3•0•Updated Oct 31, 2024Oct 31, 2024
CNAqc
Public
CNAqc - Copy Number Alteration (CNA) Quality Check package
genomics copy-number-variation karyotype peak-detection quality-check
R
•
GNU General Public License v3.0
•8•19•5•0•Updated Oct 30, 2024Oct 30, 2024
TAPACLOTH
Public
0•0•0•0•Updated Sep 21, 2024Sep 21, 2024
nextflow_modules
Public
Nextflow modules from the lab
HTML
•4•2•11•0•Updated Sep 1, 2024Sep 1, 2024
simbascule
Public
Package to generate synthetic data from the bascule generative model.
R
•0•1•0•0•Updated Aug 23, 2024Aug 23, 2024
pybascule
Public
Mutational signatures deconvolution via Bayesian NMF
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Aug 23, 2024Aug 23, 2024
INCOMMON_shiny
Public
Shiny Apps for INCOMMON
R
•0•0•0•0•Updated Jul 30, 2024Jul 30, 2024
TINC
Public
Tumour-in-Normal Contamination assessment with evolutionary theory.
genomics cancer somatic-variants evolution germline contamination
R
•2•5•0•0•Updated Apr 25, 2024Apr 25, 2024
rdevil
Public
A R Framework for Single Cell Differential Expression Analysis
Python
•
Other
•0•0•0•0•Updated Feb 7, 2024Feb 7, 2024
CONGASp_supplementary_data
Public
Jupyter Notebook
•0•1•0•0•Updated Nov 12, 2023Nov 12, 2023
congas
Public
A set of Pyro models and functions to infer CNA from scRNA-seq data
Python
•
GNU General Public License v3.0
•0•11•0•3•Updated Aug 14, 2023Aug 14, 2023
pydevil
Public
A Python Framework for Single Cell Differential Expression ANalysis
Python
•
MIT License
•0•0•0•0•Updated Jun 22, 2023Jun 22, 2023
evoverse_reproducibility
Public
A repository to store and share code developed for the evoverse paper
MIT License
•0•0•0•0•Updated Apr 20, 2023Apr 20, 2023
revolver
Public
REVOLVER - Repeated Evolution in Cancer
clustering phylogenetic-trees cancer-genomics transfer-learning cancer-evolution
R
•25•65•0•1•Updated Dec 25, 2022Dec 25, 2022
VIBER
Public
VIBER - Variational Binomial Mixtures
clustering mixture-model variational-inference nonparametric binomial-distribution
HTML
•2•2•0•0•Updated Jul 13, 2022Jul 13, 2022
keap1_classifier
Public
A classifier for clonal KEAP1 mutations.
R
•0•0•0•0•Updated Jun 20, 2022Jun 20, 2022
easypar
Public
Easy parallelisation of R computations.
parallel-computing multi-core lsf-jobs slurm-cluster r parallel
R
•
GNU General Public License v3.0
•0•2•2•0•Updated May 30, 2022May 30, 2022