Pinned Repositories
5-virus-mix
Benchmarking data sets for haplotype reconstruction methods, sequenced with Illumina MiSeq, 454/Roche GSJunior, and Pacific Biosciences
bmi
Mutual information estimators and benchmark
haploclique
Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
NGS-pipe
NGS-pipe: next-generation sequencing pipelines for precision oncology
scDEF
Deep exponential families for single-cell data.
SCICoNE
Single-cell copy number calling and event history reconstruction.
SCIPhI
SCITE
shorah
Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)
V-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Computational Biology Group (CBG)'s Repositories
cbg-ethz/V-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
cbg-ethz/bmi
Mutual information estimators and benchmark
cbg-ethz/scDEF
Deep exponential families for single-cell data.
cbg-ethz/SCICoNE
Single-cell copy number calling and event history reconstruction.
cbg-ethz/cojac
cbg-ethz/VILOCA
VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data
cbg-ethz/cowwid
Procedure used fro the surveillance of SARS-CoV-2 genomic variants in wastewater.
cbg-ethz/pangolin
BSSE COVID-19 sequencing of test swab samples
cbg-ethz/oncotree2vec
A method for embedding and clustering of tumor mutation trees.
cbg-ethz/LolliPop
Deconvolution for Wastewater Genomics
cbg-ethz/mnem
Mixture Nested Effects Models - https://doi.org/10.1093/bioinformatics/bty602 - https://bioconductor.org/packages/mnem
cbg-ethz/mt-SCITE
Tree inference from mitochondrial mutations
cbg-ethz/pMHN
Personalised mutual hazard networks: fixed effects in cancer progression modeling
cbg-ethz/CTC-SCITE
Computational method and analyses to study the clonality of circulating tumor cell clusters
cbg-ethz/Jnotype
Probabilistic modeling of high-dimensional binary data in JAX
cbg-ethz/nempi
Nested Effects Models based Perturbation Inference - https://doi.org/10.1093/bioinformatics/btab113 - https://bioconductor.org/packages/nempi
cbg-ethz/SARS-CoV-2-wastewater-sample-processing-VILOCA
wastewater-sample-processing-VILOCA
cbg-ethz/epiNEM
Epistatic Nested Effects Models - https://doi.org/10.1371/journal.pcbi.1005496 - https://bioconductor.org/packages/epiNEM/
cbg-ethz/GSoD-2024
Google Season of Docs 2024
cbg-ethz/myeloid-clustering
This repository contains supplementary information, data and code for the manuscript: Bayer et al. 2023, "Network-based clustering unveils interconnected landscapes of genomic and clinical features across myeloid malignancies"
cbg-ethz/sr2silo
Wrangling short-read sequencing data for import into SILO
cbg-ethz/covvfit
Fitness estimates of SARS-CoV-2 variants
cbg-ethz/lollipop-in-cloud
On the fly variant deconvolution running in the cloud for on demand user requests.
cbg-ethz/mixmax
cbg-ethz/oncotreeVIS
An interactive graphical user interface for visualizing mutation tree cohorts.
cbg-ethz/SCITE-RNA
cbg-ethz/tupro-evolutionary-landscapes
cbg-ethz/UsefulGnom
Useful Genomic Tools
cbg-ethz/viloca_applications
This repo contains applications of the tool VILOCA.
cbg-ethz/vpipe-biohack24-frontend
Cloudification of V-Pipe: Frontend for the Biohackathon 2024