Restore DESCRIPTION

DESCRIPTION

@@ -21,6 +21,11 @@ Depends:
     R (>= 4.3)
 Suggests:
     MsCoreUtils,
+    xcms (>= 4.1.5),
+    Spectra (>= 1.11.10),
+    MsExperiment,
+    MsIO,
+    MsBackendMetaboLights,
     readxl,
     limma,
     matrixStats,

vignettes/a-end-to-end-untargeted-metabolomics.qmd

@@ -2,9 +2,9 @@
 title: "Complete end-to-end LC-MS/MS Metabolomic Data analysis"
 format: html
 tbl-cap-location: bottom
+editor: visual
 minimal: true
 date: 'Compiled: `r format(Sys.Date(), "%B %d, %Y")`'
-bibliography: references.bib
 vignette: >
   %\VignetteIndexEntry{Complete end-to-end LC-MS/MS Metabolomic Data analysis}
   %\VignetteEngine{quarto::html}
@@ -1713,7 +1713,7 @@ Javascript as well as loaded easily back into R.
 # d <- file.path(tempdir(), "objects/lcms1")
 # saveMsObject(lcms1, AlabasterParam(path = d))
 #for now let's do R object because the previous method is not implemented yet.
-#save(lcms1, file = "preprocessed_lcms1.RData")
+save(lcms1, file = "preprocessed_lcms1.RData")
 ```
 
 # Data normalization

vignettes/dataset-investigation.qmd

@@ -1,23 +1,21 @@
 ---
 title: "Dataset investigation: What to do when you get your data"
 format: html
+editor: visual
 minimal: true
+date: 'Compiled: `r format(Sys.Date(), "%B %d, %Y")`'
 vignette: >
   %\VignetteIndexEntry{Dataset investigation: What to do when you get your data}
   %\VignetteEngine{quarto::html}
   %\VignetteEncoding{UTF-8}
-knitr:
-  opts_chunk:
-    collapse: true
-    comment: '#>'
 ---
 
 ## In Construction
 
-```{r}
+```{r setup, include=FALSE}
 library(knitr)
 library(quarto)
-#knitr::opts_knit$set(root.dir = './')
+knitr::opts_knit$set(root.dir = './')
 ```
 
 # Introduction