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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

bmix

BMix is a novel probabilistic method based on a constrained three-component mixture, which identifies high confidence T-to-C substitutions in PAR-CLIP data, and, based on these, reports putative RNA-protein cross-link sites.

bnclustomics

bnpc

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

cancer-type-prediction-from-tumour-dna

clustnet

Network-based clustering

cojac

compass

conda_stats_gather

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

consensusfixer

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

covvfit

Fitness estimates of SARS-CoV-2 variants

cowwid

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

ctc-scite

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

dbnclass

dce

Finding the causality in biological pathways

dcv-evolution-data-processing

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

demotape

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

epinem

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

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.

fairclust

geneaccord

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

gesper

Gene-Specific Phenotype EstimatoR

graphclust_neurips

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

h-cbn2-comparison-test

Snakemake pipeline to compare two H-CBN models

haploclique

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

hcc

hdl-x

igb

IGB is a R script for computing individualized genetic barrier

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.