Discover cbg-ethz/PrimerID Open Source project

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

130

NGS-pipe

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

104

shorah

Mutual information estimators and benchmark

bmi

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

haploclique

SCIPhI

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

5-virus-mix

SCICoNE

Single-cell copy number calling and event history reconstruction.

SCITE

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

BnpC

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

ConsensusFixer

Java

scDEF

Deep exponential families for single-cell data.

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

QuasiRecomb

Java

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

MATLAB

cojac

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

VILOCA

Map single-cell transcriptomes to copy number evolutionary trees.

SCATrEx

Finding the causality in biological pathways

dce

COMPASS

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

smallgenomeutilities

Inference in Bayesian Networks with R

SGS

pybda

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

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

ngshmmalign

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

cowwid

scIsoPrep

Single-cell Iso Prep

BSSE COVID-19 sequencing of test swab samples

predictability_of_cancer_evolution

WES_Cancer_Sim

pangolin

Shell

pareg

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

infSCITE

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

TreeMHN

scSomMerClock

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

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.

InDelFixer

Java

SCIPhIN

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

metMHN

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

clustNet

Network-based clustering

graphClust_NeurIPS

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.

Inference and analysis of mutation trees in Python

PYggdrasil

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

MC-CBN

LolliPop

Deconvolution for Wastewater Genomics

Tree inference from mitochondrial mutations

mt-SCITE

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

TiMEx

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

MATLAB

gespeR

Gene-Specific Phenotype EstimatoR

timeseriesNEM

HDL-X

pMHN

Personalised mutual hazard networks

Inverse reinforcement learning for mutation trees

netprioR

PhIRL

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

SARS-CoV-2_Analysis

Deep hierarchical models combined with Markov random fields.

oncotree2vec

JavaScript

cancer-type-prediction-from-tumour-DNA

shm

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

GeneAccord

openproblems2021

Analysis of high-throughput genetic perturbation screens in R.

perturbatr

Jnotype

Exploratory analysis of binary data in JAX

wastewater-sample-processing-VILOCA

bnclustOmics

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

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

QuasiFit

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.

ObservationMHN

epistasis-formulas

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

nempi

scdna-pipe

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

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"

myeloid-clustering

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