Caravagna Lab

The Cancer Data Science Laboratory at the University of Trieste, Italy. PI Giulio Caravagna.

Trieste

Pinned Repositories

BMix
Binomial and Beta-Binomial mixture models for counts data.
Language:HTML5 2 10
CNAqc
CNAqc - Copy Number Alteration (CNA) Quality Check package
Language:R17 4 298
congas
A set of Pyro models and functions to infer CNA from scRNA-seq data
Language:Python11 1 40
CONGASp
Language:Python4 2 10
ctree
Clone trees for Cancer Evolution studies from bulk sequencing data.
Language:R5 3 22
mobster
Model-based subclonal deconvolution from bulk sequencing.
Language:HTML33 8 258
rcongas
rcongas
Language:R7 2 361
revolver
REVOLVER - Repeated Evolution in Cancer
Language:R64 7 4025
TINC
Tumour-in-Normal Contamination assessment with evolutionary theory.
Language:R4 3 62
VIBER
VIBER - Variational Binomial Mixtures
Language:HTML2 4 12

Caravagna Lab's Repositories

caravagnalab/revolver
REVOLVER - Repeated Evolution in Cancer
Language:R64 7 4025
caravagnalab/mobster
Model-based subclonal deconvolution from bulk sequencing.
Language:HTML33 8 258
caravagnalab/CNAqc
CNAqc - Copy Number Alteration (CNA) Quality Check package
Language:R17 4 298
caravagnalab/congas
A set of Pyro models and functions to infer CNA from scRNA-seq data
Language:Python11 1 40
caravagnalab/rcongas
rcongas
Language:R7 2 361
caravagnalab/CONGASp
Language:Python4 2 10
caravagnalab/TINC
Tumour-in-Normal Contamination assessment with evolutionary theory.
Language:R4 3 62
caravagnalab/nextflow_modules
Nextflow modules from the lab
Language:HTML3 1 284
caravagnalab/devil
devil
Language:R2 2 11
caravagnalab/easypar
Easy parallelisation of R computations.
Language:R2 3 6
caravagnalab/rRACES
R wrapper for the RACES package
Language:C++2 2 1201
caravagnalab/VIBER
VIBER - Variational Binomial Mixtures
Language:HTML2 4 12
caravagnalab/bascule
Detecting mutational signatures via bayesian inference and a reference catalog
Language:R1 5 21
caravagnalab/caravagnalab.github.io
Landing repository for GitHub Pages
Language:HTML1 2 01
caravagnalab/CONGASp_supplementary_data
Language:Jupyter Notebook1 2 00
caravagnalab/INCOMMON
Inference of copy number and mutation multiplicity in oncology
Language:R1 3 31
caravagnalab/lineaGT
Lineage inference from Gene Therapy assays with insertional mutagenesis and somatic mutations
Language:R1 3 0
caravagnalab/pylineaGT
A Pyro model to perform lineage inference from Gene Therapy assays
Language:Python1 2 0
caravagnalab/simbascule
Package to generate synthetic data from the bascule generative model.
Language:R1 2 0
caravagnalab/TAPACLOTH
Targeted panel-oriented test for clonality and heterozygosity
Language:R1 1 01
caravagnalab/tumourevo
Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
1 2 112
caravagnalab/INCOMMON_shiny
Shiny Apps for INCOMMON
Language:R0 2 00
caravagnalab/rRACES-examples
Language:HTML0 2 10
caravagnalab/biPOD
Bayesian inference for population dynamics
Language:R3 1
caravagnalab/evoverse_reproducibility
A repository to store and share code developed for the evoverse paper
2 0
caravagnalab/keap1_classifier
A classifier for clonal KEAP1 mutations.
Language:R2 0
caravagnalab/pybascule
Mutational signatures deconvolution via Bayesian NMF
Language:Python4 01
caravagnalab/pydevil
A Python Framework for Single Cell Differential Expression ANalysis
Language:Python2 0
caravagnalab/rdevil
A R Framework for Single Cell Differential Expression Analysis
Language:Python2 0
caravagnalab/tickTack
Timing Inference for Copy number alterations: Tracking Alterations in Cancer Karyotypes
Language:R2 0