{ "_id": "6a1aca6e1d7bb097a09dd43b", "Package": "MIRit", "Title": "Integrate microRNA and gene expression to decipher pathway\ncomplexity", "Version": "1.9.0", "Date": "2023-11-23", "Authors@R": "c(\nperson(\"Jacopo\", \"Ronchi\", email = \"jacopo.ronchi@unimib.it\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5520-4631\")),\nperson(\"Maria\", \"Foti\", email = \"maria.foti@unimib.it\",\nrole = c(\"fnd\"), comment = c(ORCID = \"0000-0002-4481-1900\")))", "Description": "MIRit is an R package that provides several methods for\ninvestigating the relationships between miRNAs and genes in\ndifferent biological conditions. In particular, MIRit allows to\nexplore the functions of dysregulated miRNAs, and makes it\npossible to identify miRNA-gene regulatory axes that control\nbiological pathways, thus enabling the users to unveil the\ncomplexity of miRNA biology. 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performMirnaDE() and performGeneDE() functions", "Advanced parameters", "Add differential expression results from other technologies", "Visualize differentially expressed features", "Access differential expression tables", "Create a volcano plot for miRNAs and genes", "Produce differential expression bar plots", "Functional enrichment analysis", "Available approaches: ORA, GSEA and CAMERA", "Available databases and categories", "Supported species", "Perform functional enrichment with the enrichGenes() function", "Visualize enriched sets", "Access results table", "Enrichment dot plots and bar plots", "Other plots for GSEA", "Retrieve miRNA targets", "Databases with miRNA-mRNA interactions", "The mirDIP approach", "Download predicted and validated interactions with getTargets()", "Assess the effects of miRNAs on target genes", "Correlation analysis for paired data", "Statistical correlation coefficients", "Perform a correlation analysis in MIRit", "Account for the group effect in 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