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basilica

Detecting mutational signatures via bayesian inference and a reference catalog

bioconda-recipes

Conda recipes for the bioconda channel.

bipod

Bayesian inference for population dynamics

bmix

Binomial and Beta-Binomial mixture models for counts data.

caravagnalab.github.io

Landing repository for GitHub Pages

cnaqc

CNAqc - Copy Number Alteration (CNA) Quality Check package

cnaqc_datasets

Datasets for the CNAqc paper

congas

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

congasp

congasp_supplementary_data

ctree

Clone trees for Cancer Evolution studies from bulk sequencing data.

devil

devil

easypar

Easy parallelisation of R computations.

evoverse_reproducibility

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

incommon

Inference of copy number and mutation multiplicity in oncology

incommon_shiny

Shiny Apps for INCOMMON

keap1_classifier

A classifier for clonal KEAP1 mutations.

lineagt

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

mobster

Model-based subclonal deconvolution from bulk sequencing.

nextflow_modules

Nextflow modules from the lab

nf-core-evoverse

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

pybasilica

Mutational signatures deconvolution via Bayesian NMF

pydevil

A Python Framework for Single Cell Differential Expression ANalysis

pylineagt

A Pyro model to perform lineage inference from Gene Therapy assays

rcongas

rcongas

rcongas_test

rdevil

A R Framework for Single Cell Differential Expression Analysis

revolver

REVOLVER - Repeated Evolution in Cancer

rraces

R wrapper for the RACES package

rraces-examples