ArticleBioinformatics (Oxford, England)2024
InstaPrism: an R package for fast implementation of BayesPrism.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
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- cellGeometry: ultra-fast single-cell deconvolution of bulk RNA-Seq using a geometric solution.Nature communications · 2026Article
- Network-based machine learning to identify biomarkers for systemic lupus erythematosus.BMC biology · 2026Article
- Single-nucleus profiling reveals age-associated remodeling opposed by parity in the postmenopausal human ovary.bioRxiv : the preprint server for biology · 2026Article
- The transcriptome of CD14The European respiratory journal · 2026Article
- SpaNiche: spatial niche analysis to explore colocalization patterns and cellular interactions in spatial transcriptomics data.Genome biology · 2026Article
- Transcriptomic subtypes in high-grade serous ovarian cancer are driven by tumor cellular composition.bioRxiv : the preprint server for biology · 2026Article
- Integrating single-cell and single-nucleus datasets improves bulk RNA-seq deconvolution.Cell reports methods · 2026Article
- Integration of Bulk and Single-Cell RNA Sequencing Analyses in Biomedicine.International journal of molecular sciences · 2026Review
- Evaluating reference-mixture matching in cell-type deconvolution with single-cell RNA-seq references.Briefings in bioinformatics · 2026Article
- Deconvolved tumor adipocyte proportions and high grade serous ovarian carcinoma survival.bioRxiv : the preprint server for biology · 2026Article
- Helicobacter pylori-Induced Inflammatory Cancer Transformation Microenvironment Drives Gastric Carcinogenesis.Cellular and molecular gastroenterology and hepatology · 2026Article
- WDR82 suppresses breast cancer progression by inhibiting ERK-driven chemokine expression and neutrophil infiltration.International journal of biological sciences · 2026Article
- Host biological sex directs immune control of theFrontiers in immunology · 2026Article
- From Raw Data to Biological Insights: A Practical Guide for Spatial Transcriptomics Analysis in R and Python.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A robust workflow to benchmark deconvolution of multi-omic data.Genome biology · 2025Article
- Form and function of actin impacts actin health and aging.bioRxiv : the preprint server for biology · 2025Article
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2 authors.
Funding
Abstract
summaryComputational cell-type deconvolution is an important analytic technique for modeling the compositional heterogeneity of bulk gene expression data. A conceptually new Bayesian approach to this problem, BayesPrism, has recently been proposed and has subsequently been shown to be superior in accuracy and robustness against model misspecifications by independent studies; however, given that BayesPrism relies on Gibbs sampling, it is orders of magnitude more computationally expensive than standard approaches. Here, we introduce the InstaPrism package which re-implements BayesPrism in a derandomized framework by replacing the time-consuming Gibbs sampling step with a fixed-point algorithm. We demonstrate that the new algorithm is effectively equivalent to BayesPrism while providing a considerable speed and memory advantage. Furthermore, the InstaPrism package is equipped with a precompiled, curated set of references tailored for a variety of cancer types, streamlining the deconvolution process. AVAILABILITY AND IMPLEMENTATION: The package InstaPrism is freely available at: https://github.com/humengying0907/InstaPrism. The source code and evaluation pipeline used in this paper can be found at: https://github.com/humengying0907/InstaPrismSourceCode.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.