@@ -4,7 +4,7 @@ This is an R program to visualize and analyze -omics data such as those from mic
...
@@ -4,7 +4,7 @@ This is an R program to visualize and analyze -omics data such as those from mic
## Current version: V2.0c. Tested R version: 4.0.2.
## Current version: V2.1. Tested R version: 4.3.2.
**Highlighted changes:** Metabolite Set Enrichment Analysis (MSEA), Pathway Analysis (MSPA), and Joint-Pathway Analysis (JointPA) are 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 changes:** Metabolite Set Enrichment Analysis (MSEA), Pathway Analysis (MSPA), and Joint-Pathway Analysis (JointPA) are 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.
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@@ -28,10 +28,6 @@ sh /path_to_the_program/run_analysis.sh /input_path/your_data_file.xlsx /outp
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@@ -28,10 +28,6 @@ sh /path_to_the_program/run_analysis.sh /input_path/your_data_file.xlsx /outp
* For the first time running this program, you will need internet access so that the program can auto-download necessary R packages. If you want to install packages to a different directory, find the following line from the ODA.R and change it.
```
myLibPath='~/R/4.0.2-gccmkl' #Change this to your own library path if necessary.
```
## Examples: See the Examples folder for typical analysis settings and output files (more to be added).
## Examples: See the Examples folder for typical analysis settings and output files (more to be added).
