@@ -7,6 +7,7 @@ This is an R program to visualize and analyze -omics data such as those from met
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@@ -7,6 +7,7 @@ This is an R program to visualize and analyze -omics data such as those from met
## Current version: V2.2.1. Tested R version: 4.3.2.
## Current version: V2.2.1. Tested R version: 4.3.2.
Updates in V2.2.1: A Coefficient of Variation (CV) column was added for the raw and normalized data sheets. clusterProfiler QEA and ORA analyses were added for the "Other" data type with a customized DB in the .gmt format. log2 fold changes were added to comparison sheets to facilitate the clusterProfiler QEA analysis.
Updates in V2.2.1: A Coefficient of Variation (CV) column was added for the raw and normalized data sheets. clusterProfiler QEA and ORA analyses were added for the "Other" data type with a customized DB in the .gmt format. log2 fold changes were added to comparison sheets to facilitate the clusterProfiler QEA analysis.
**Highlighted updates in V2.2:** Bulk RNA-seq analysis starting from a raw count table was added. DESeq2 is used for bulk RNA-seq data normalization and differential tests. clusterProfiler ORA and QEA analyses were added for gene/protein data. PLS-DA plot was added. Spearman and Kendall correlation plots were added. Analysis without erasing previous results was enabled. Bug fixes.
**Highlighted updates in V2.2:** Bulk RNA-seq analysis starting from a raw count table was added. DESeq2 is used for bulk RNA-seq data normalization and differential tests. clusterProfiler ORA and QEA analyses were added for gene/protein data. PLS-DA plot was added. Spearman and Kendall correlation plots were added. Analysis without erasing previous results was enabled. Bug fixes.
**Highlighted updates in V2.1:** Metabolite Set Enrichment Analysis (MSEA), Pathway Analysis (MSPA), and Joint-Pathway Analysis (JointPA) were implemented using MetaboAnalystR 3.0.3. If a list of metabolite IDs is supplied, the Over Representation Analysis (ORA) can be done. If a differential test is specified, the Quantitative Enrichment Analysis (QEA) can be done. To do the analysis, metabolites need to be HMDB IDs or KEGG IDs. Alternatively, features can be metabolite names available in the MetaboAnalyst's compound database. See [MetaboAnalyst](https://www.metaboanalyst.ca/) for details about MSEA, MSPA, and JointPA.
**Highlighted updates in V2.1:** Metabolite Set Enrichment Analysis (MSEA), Pathway Analysis (MSPA), and Joint-Pathway Analysis (JointPA) were implemented using MetaboAnalystR 3.0.3. If a list of metabolite IDs is supplied, the Over Representation Analysis (ORA) can be done. If a differential test is specified, the Quantitative Enrichment Analysis (QEA) can be done. To do the analysis, metabolites need to be HMDB IDs or KEGG IDs. Alternatively, features can be metabolite names available in the MetaboAnalyst's compound database. See [MetaboAnalyst](https://www.metaboanalyst.ca/) for details about MSEA, MSPA, and JointPA.
