BayICE: a Bayesian hierarchical model for semireference-based deconvolution of bulk transcriptomic data

DOI10.1214/20-AOAS1376zbMATH Open1475.62266OpenAlexW3136741255MaRDI QIDQ2233183FDOQ2233183

Authors: An-Shun Tai, Wen-Ping Hsieh, George C. Tseng 

Publication date: 14 October 2021

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1214/20-aoas1376

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zbMATH Keywords

gene expressionstochastic search variable selectionhierarchical Bayesiancell proportionsemi-reference-based deconvolution

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10)

Cites Work

• Baycount: a Bayesian decomposition method for inferring tumor heterogeneity using RNA-seq counts
• Spike and slab variable selection: frequentist and Bayesian strategies
• Spike and Slab Gene Selection for Multigroup Microarray Data
• A Bayesian False Discovery Rate for Multiple Testing

Cited In (7)

• ICeD-t provides accurate estimates of immune cell abundance in tumor samples by allowing for aberrant gene expression patterns
• Loss-Function Learning for Digital Tissue Deconvolution
• A Bayesian Multivariate Mixture Model for High Throughput Spatial Transcriptomics
• BayICE
• Geometric structure guided model and algorithms for complete deconvolution of gene expression data
• Estimating Cell Type Composition Using Isoform Expression One Gene at a Time
• Immune classification of osteosarcoma

Uses Software

• R
• spikeslab
• BayCount
• dtangle
• ISOpureR

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