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
ConsensusFixer
Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.
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
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/SCICoNE
Single-cell copy number calling and event history reconstruction.
cbg-ethz/BnpC
Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates
cbg-ethz/cojac
cbg-ethz/COMPASS
cbg-ethz/scDEF
Deep exponential families for single-cell data.
cbg-ethz/SCATrEx
Map single-cell transcriptomes to copy number evolutionary trees.
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/TreeMHN
Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees
cbg-ethz/clustNet
Network-based clustering
cbg-ethz/LolliPop
Deconvolution for Wastewater Genomics
cbg-ethz/metMHN
This is a adaptation to MHN so that it works on metastasis
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/oncotree2vec
cbg-ethz/pMHN
Personalised mutual hazard networks
cbg-ethz/PYggdrasil
Inference and analysis of mutation trees in Python
cbg-ethz/LongSom
LongSom tool for long-reads
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/demoTape
Computational demultiplexing of targeted single-cell sequencing (tapestri) data
cbg-ethz/epiNEM
Epistatic Nested Effects Models - https://doi.org/10.1371/journal.pcbi.1005496 - https://bioconductor.org/packages/epiNEM/
cbg-ethz/Jnotype
Exploratory analysis of binary data in JAX
cbg-ethz/covvfit
Fitness estimates of SARS-CoV-2 variants
cbg-ethz/DCV-Evolution-Data-Processing
Workflow for the processsing of data from the DCV evolutionary experiments.
cbg-ethz/oncotreeVIS
cbg-ethz/viloca_applications
This repo contains applications of the tool VILOCA.