Computational Biology Group (CBG)

V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

bmi

Mutual information estimators and benchmark

scDEF

Deep exponential families for single-cell data.

SCICoNE

Single-cell copy number calling and event history reconstruction.

BnpC

Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates

cojac

COMPASS

VILOCA

VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data

SCATrEx

Map single-cell transcriptomes to copy number evolutionary trees.

smallgenomeutilities

smallgenomeutilities is a collection of Python scripts to convert alignments between different reference genomes.

pybda

:computer::computer::computer: A commandline tool for analysis of big biological data sets for distributed HPC clusters.

cowwid

Procedure used fro the surveillance of SARS-CoV-2 genomic variants in wastewater.

pangolin

BSSE COVID-19 sequencing of test swab samples

LongSom

LongSom tool for long-reads

LolliPop

Deconvolution for Wastewater Genomics

metMHN

This is a adaptation to MHN so that it works on metastasis

mnem

Mixture Nested Effects Models - https://doi.org/10.1093/bioinformatics/bty602 - https://bioconductor.org/packages/mnem

mt-SCITE

Tree inference from mitochondrial mutations

CTC-SCITE

Computational method and analyses to study the clonality of circulating tumor cell clusters

Jnotype

Exploratory analysis of binary data in JAX

ObservationMHN

SARS-CoV-2-wastewater-sample-processing-VILOCA

wastewater-sample-processing-VILOCA

scdna-pipe

Python data analysis pipeline for single cell copy number event history reconstruction

epiNEM

Epistatic Nested Effects Models - https://doi.org/10.1371/journal.pcbi.1005496 - https://bioconductor.org/packages/epiNEM/

conda_stats_gather

Used to track downloads of bioconda packages used by V-pipe, see: https://cbg-ethz.github.io/V-pipe/pipeline/

covvfit

Fitness estimates of SARS-CoV-2 variants

DCV-Evolution-Data-Processing

Workflow for the processsing of data from the DCV evolutionary experiments.

MARCS

oncotreeVIS

viloca_applications

This repo contains applications of the tool VILOCA.