· 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
Abstract Accurate cell annotation is a primary challenge in spatial transcriptomics (ST). Current approaches primarily rely on label transfer from single-cell RNA sequencing (scRNA-seq) reference or marker-based clustering. While these methods are widely used, they have critical limitations. Label transfer approaches d...
Hong-Hao Bi, Wenjie Cai, Pan Wang et al.· Nucleic Acids Research· 0 citations
Single-cell RNA-sequencing measurements are uniquely well-poised to identify coregulated gene transcription. Coregulation should be apparent as correlation of expression levels, but at which unit to quantify expression for calculation of correlations is not clear. To enable evaluation of normalization methods for ident...
Feature selection is critical for resolving cell-type heterogeneity in single-cell RNA sequencing (scRNA-seq). DUBStepR (Determining the Underlying Basis using Stepwise Regression) is a widely used gene selection method for scRNA-seq designed to identify feature genes that maximize cell-type separation. DUBStepR has be...
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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