cbg-ethz/myeloid-clustering

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cbg-ethz/myeloid-clustering

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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"

V-pipe

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

Jupyter Notebook

NGS-pipe

NGS-pipe: next-generation sequencing pipelines for precision oncology

shorah

Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)

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.

SCIPhI

5-virus-mix

Benchmarking data sets for haplotype reconstruction methods, sequenced with Illumina MiSeq, 454/Roche GSJunior, and Pacific Biosciences

SCICoNE

Single-cell copy number calling and event history reconstruction.

SCITE

BnpC

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

ConsensusFixer

Computes a consensus sequence with wobbles, ambiguous bases, and in-frame insertions, from a NGS read alignment.

scDEF

Deep exponential families for single-cell data.

QuasiRecomb

Probabilistic inference of viral quasispecies subject to recombination (viral haplotype reconstruction).

pancancer-clustering

Bayesian network modelling of mutational interactions identifies novel cancer subgroups

netics

NetICS: network-based integration of multi-omics data for prioritizing cancer genes

cojac

Jupyter Notebook

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.

dce

Finding the causality in biological pathways

COMPASS

smallgenomeutilities

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

SGS

Inference in Bayesian Networks with R

pybda

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

ngshmmalign

ngshmmalign is a profile HMM aligner for NGS reads designed particularly for small genomes (such as those of RNA viruses like HIV-1 and HCV) that experience substantial biological insertions and deletions

cowwid

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

Jupyter Notebook

scIsoPrep

Single-cell Iso Prep

predictability_of_cancer_evolution

WES_Cancer_Sim

pangolin

BSSE COVID-19 sequencing of test swab samples

pareg

Pathway enrichment computations using a regularized regression approach to incorporate inter-pathway relations in the statistical model.

infSCITE

TreeMHN

Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees

scSomMerClock

Test for a molecular clock based on the phylogenetic tree inferred from single-cell DNA sequenzing data

InDelFixer

Iterative and very sensitive Next-Generation Sequencing (NGS) sequence alignment software. Accounting for large deletions and removes indels, causing frame shifts. In addition, only specific regions can be considered.

PrimerID

Here we analyse the PrimerID protocol in all its gory details.

SCIPhIN

metMHN

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

clustNet

Network-based clustering

graphClust_NeurIPS

Network-Based Clustering of Pan-Cancer Data Accounting for Clinical Covariates

slidr

An R package for identification of synthetic lethal partners for mutations from large perturbation screens.

PredictHaplo

This software aims at reconstructing haplotypes from next-generation sequencing data.

PYggdrasil

Inference and analysis of mutation trees in Python

MC-CBN

MC-CBN performs large-scale inference on conjunctive Bayesian networks

LolliPop

Deconvolution for Wastewater Genomics

Jupyter Notebook

mt-SCITE

Tree inference from mitochondrial mutations

Jupyter Notebook

TiMEx

Bioconductor package for finding mutually exclusive groups of alterations in large cancer datasets

mnem

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

SynNet

Toolbox for design and optimization of miRNA-based synthetic classifier pathways

gespeR

Gene-Specific Phenotype EstimatoR

timeseriesNEM

HDL-X

pMHN

Personalised mutual hazard networks

netprioR

PhIRL

Inverse reinforcement learning for mutation trees

SARS-CoV-2_Analysis

A Snakemake workflow for large-scale SARS-CoV-2 analyses.

oncotree2vec

cancer-type-prediction-from-tumour-DNA

shm

Deep hierarchical models combined with Markov random fields.

GeneAccord

GeneAccord: An R package to detect patterns of mutual exclusivity and co-occurrence on the clone level in a cohort of cancer patients

openproblems2021

perturbatr

Analysis of high-throughput genetic perturbation screens in R.

Jnotype

Exploratory analysis of binary data in JAX

bnclustOmics

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

wastewater-sample-processing-VILOCA

Jupyter Notebook

QuasiFit

QuasiFit is a Bayesian MCMC sampler for inferring fitness landscapes in the quasispecies model subject to mutation-selection equilibrium.

ObservationMHN

epistasis-formulas

Computes higher-order interactions such as 2-way, 3-way,…, n-way interaction coordinates and some circuits in the n-locus case taking as input 2^n experimental measurements.

nempi

Nested Effects Models based Perturbation Inference - https://doi.org/10.1093/bioinformatics/btab113 - https://bioconductor.org/packages/nempi

scdna-pipe

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

fairClust

DBNclass

pcNEM

pathTiMEx

pathTiMEx is a model for the joint inference of mutually exclusive pathways and the dependencies among them in carcinogenesis

demoTape

Computational demultiplexing of targeted single-cell sequencing (tapestri) data

TMixClust

tree-embeddings

epiNEM

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