PathVisio

MetaboAnalyst — comprehensive R package and web platform for metabolomics data analysis and interpretation. Provides statistical analysis (t-test, ANOVA, PCA, PLS-DA), pathway analysis (KEGG, SMPDB),

3 shared topics • 2 shared operations

clusterProfiler — universal enrichment analysis tool for interpreting omics data using Gene Ontology, KEGG pathways, WikiPathways, Reactome, Disease Ontology, and custom gene sets. Implements over-rep

2 shared topics • 1 shared operation

Use when inferring mechanistic causal links across multiple omics layers with COSMOS (Causal Oriented Search of Multi-Omics Space). Integrates metabolomics, transcriptomics, and signaling pathway data

2 shared topics • 1 shared operation

fgsea — fast preranked gene set enrichment analysis in R using an adaptive multi-level split Monte-Carlo scheme for arbitrarily precise GSEA p-values. Provides fgsea(), fgseaMultilevel(), plotEnrichme

2 shared topics • 1 shared operation

MAGeCK-VISPR — comprehensive CRISPR screen analysis framework combining MAGeCK statistical testing (RRA and MLE algorithms) with VISPR interactive visualization. Supports sgRNA count generation from F

2 shared topics • 1 shared operation