Caravagna Lab

revolver

REVOLVER - Repeated Evolution in Cancer

mobster

Model-based subclonal deconvolution from bulk sequencing.

CNAqc

CNAqc - Copy Number Alteration (CNA) Quality Check package

congas

A set of Pyro models and functions to infer CNA from scRNA-seq data

rcongas

rcongas

CONGASp

TINC

Tumour-in-Normal Contamination assessment with evolutionary theory.

nextflow_modules

Nextflow modules from the lab

devil

devil

easypar

Easy parallelisation of R computations.

rRACES

R wrapper for the RACES package

VIBER

VIBER - Variational Binomial Mixtures

bascule

Detecting mutational signatures via bayesian inference and a reference catalog

caravagnalab.github.io

Landing repository for GitHub Pages

CONGASp_supplementary_data

INCOMMON

Inference of copy number and mutation multiplicity in oncology

lineaGT

Lineage inference from Gene Therapy assays with insertional mutagenesis and somatic mutations

pylineaGT

A Pyro model to perform lineage inference from Gene Therapy assays

simbascule

Package to generate synthetic data from the bascule generative model.

TAPACLOTH

Targeted panel-oriented test for clonality and heterozygosity

tumourevo

Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

INCOMMON_shiny

Shiny Apps for INCOMMON

biPOD

Bayesian inference for population dynamics

evoverse_reproducibility

A repository to store and share code developed for the evoverse paper

keap1_classifier

A classifier for clonal KEAP1 mutations.

pybascule

Mutational signatures deconvolution via Bayesian NMF

pydevil

A Python Framework for Single Cell Differential Expression ANalysis

rdevil

A R Framework for Single Cell Differential Expression Analysis

rRACES-examples

tickTack

Timing Inference for Copy number alterations: Tracking Alterations in Cancer Karyotypes