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Software
bayesReact
BayesReact (BAYESian modeling of Regular Expression ACTivity) is a fully Bayesian and unsupervised generative model, which enables miRNA and other motif-mediated regulatory activity inference from sparse single-cell gene expression data. (2026).
LIONHEART
A method for detecting cancer from whole genome sequenced plasma cell-free DNA (2025)
DREAMS
Deep Read-level Error Model for Sequencing data. Includes modules for ctDNA variant calling and cancer detection (2022)
KMERPAPA
Bioinformatic tool to calculate a "k-mer pattern partition" from position specific k-mer counts (2021)
NMIBC CLASSIFIER
An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer (2021)
CSG PREDICTION
Classifying cGAS-STING activity links chromosomal instability with immunotherapy response in metastatic bladder cancer (2021)
METHCORR SOFTWARE
Infer iRNA expression scores for 11 cancer types from DNA methylation 450K chip β-values (2020)
REGMEX
Regmex is a package for evaluation of motif rank correlation in a list of ranked DNA or RNA sequences (2018)
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NORMFINDER
NormFinder is an algorithm for identifying the optimal normalization gene among a set of candidates (2004)
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