scMontage

scMontage performs gene expression similarity searches on single-cell RNA-seq (scRNA-seq) datasets to identify cells with similar transcriptional profiles.

Key Features:

• Gene expression similarity search: Compares a query gene expression profile against large single-cell datasets to find similar cells or cell states.
• Spearman's rank correlation: Computes similarity using Spearman's rank correlation coefficient.
• Statistical stabilization and testing: Applies Fisher's Z-transformation to stabilize variance of correlation coefficients and performs Z-tests to assess significance.
• Integration with SHOGoiN database: Links search results to the SHOGoiN database (http://shogoin.stemcellinformatics.org) for additional cell-type information.
• Rapid large-scale comparison: Enables rapid comparison against thousands of samples, often returning results within seconds.

Scientific Applications:

• Cell type identification: Identification and annotation of cell types by matching query profiles to reference single-cell datasets.
• Detection of cellular heterogeneity: Detection and characterization of cellular heterogeneity within tissues or samples.
• Investigation of cell states and mechanisms: Investigation of cell states, developmental pathways, and disease-associated transcriptional changes.

Methodology:

Calculates Spearman's rank correlation coefficients between query and sample profiles, applies Fisher's Z-transformation to correlation values, and uses Z-tests to assess significance.