LCS v3.0 turbo & connector

Logical Clustering Turbo & Connector Suite (v3.0, MS-windows)

LCS v3.0 (turbo), the Logical Clustering Suite, is a Windows application for identifying interpretable gene-expression patterns across multi-group RNA-seq count datasets. Instead of clustering genes solely by unsupervised similarity, LCS enumerates all possible logical expression patterns across detected experimental groups and assigns genes to the phenotype pattern they best match. This enables direct discovery of biologically meaningful signatures such as genes shared by selected perturbations, excluded from others, rescued by treatment, or specific to defined combinations of conditions. The package includes both a graphical user interface and a command-line core application, supports automatic group detection from sample headers, produces annotated Excel workbooks with count matrices, logical-cluster permutation tables, diagnostic sheets, gene-universe summaries, and detailed method information, and can operate either in standalone mode using internal LCS statistics or in Bioconductor-compatible mode through R/edgeR. In edgeR mode, LCS combines logical pattern matching with RNA-seq-appropriate generalized linear model statistics, reporting edgeR logFC, fold change, P value, FDR, and expression metrics alongside internal LCS measures such as correlation distance, Welch statistics, Z score, and internal fold change. The companion LCS Connector application compares phenotype/IP gene sets across multiple LCS workbooks, quantifies statistically significant gene-set overlap and enrichment, supports optional marker-set and g annotation, and exports network tables for visualization in Cytoscape. This makes LCS suitable for exploratory pattern discovery, reproducible differential-expression workflows, cross-dataset comparison, and publication-oriented analysis of complex multi-condition experiments.

NEW: Convencience/compatibility updates to the LCS Turbo application and added Connector app for enrichment network generation (Cytoscape compatible output, see manual).

Citation:

Ma Y, Hui KL, Gelashvili Z, Niethammer P. Oxoeicosanoid signaling mediates early antimicrobial defense in zebrafish. Cell Rep. 2023 Jan 31;42(1):111974. doi: 10.1016/j.celrep.2022.111974. Epub 2023 Jan 10. PMID: 36640321; PMCID: PMC9973399.