· Methods in molecular biology· Vol 3074, pp.
69-81
· 1 citation
Medicine
TL;DR
This work presents Target-Oriented Reference Construction (TORC), a widely applicable strategy for constructing reference data from available labeled cells given a target dataset that alleviates the differences in data distribution and cell-type composition between the reference and the target.
Motivation Single-cell RNA sequencing (scRNA-seq) cluster annotation is a critical step in data analysis. Current methods are time-consuming, difficult to reproduce, or limited in tissue or species coverage. Results We developed celltypeEnrich, a cluster-level annotation tool that uses a hypergeometric test to identify...
Samuel D. Rutledge, G. Tuteja· bioRxiv· 0 citations
CARA is introduced, a cross-omics Bayesian framework that transfers cell type knowledge from scRNA-seq to scATAC-seq and detects novel cell types in single-cell DNA methylation data, demonstrating seamless extensibility to new modalities.
Lan Cao, Wenhao Zhang, Feng Zhou et al.· Genome Research· 0 citations
Binary-SPA demonstrates robust performance in challenging specimens such as bone marrow biopsies, and validation against matched COMET protein expression data confirmed strong concordance between transcriptomic- and protein-based cell identities.
Hong-Hao Bi, Wenjie Cai, Pan Wang et al.· Nucleic Acids Research· 0 citations
To enable evaluation of normalization methods for identification of coregulation, 35 scRNA-seq samples with known regulature relationships are curated and preprocessed into a catalog and results indicate implementation choices for advanced normalization methods.
Three enhancements are presented in this study: RFCell-DUBStepR, which uses random forests to capture expression-level importance; Copula-DUBStepR, which models non-linear correlations via Gaussian Copulas; and Zqt-DUBStepR, which utilizes quantile-based selection for improved gene retention.
REFCON is introduced, a deep-learning model that enables reference-free copy number profiling from scRNA-seq data collected without matched normals, and profiles pure tumors, generalizes to unseen tissues and platforms, and stays robust to cohort composition.
M. Gençtürk, A. E. Cicek· bioRxiv· 0 citations
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