fix, order file, dpendency,

DESCRIPTION

@@ -18,13 +18,14 @@ Encoding: UTF-8
 LazyData: false
 Roxygen: list(markdown = TRUE)
 Depends:
-    R (>= 4.3),
+    R (>= 4.3)
+Suggests:
+    MsCoreUtils,
     xcms (>= 4.1.5),
     Spectra (>= 1.11.10),
     MsExperiment, 
     MsIO, 
-    MsBackendMetaboLights
-Suggests:
+    MsBackendMetaboLights, 
     readxl, 
     limma,
     matrixStats,

_pkgdown.yml

@@ -6,16 +6,18 @@ template:
 navbar:
   title: Metabonaut
   left:
-  - text: Install
+  - text: Installation instruction
     href: articles/install_v0.html
   - text: Vignettes
     menu:
     - text: 'Dataset investigation: What to do when you get your data'
       href: articles/dataset-investigation.html
     - text: End-to-end workflow for untargeted metabolomics data analysis in R
-      href: articles/end-to-end-untargeted-metabolomics.html
+      href: articles/a-end-to-end-untargeted-metabolomics.html
     - text: 'Seamless Alignment: Merging New data with Existing Preprocessed Datasets'
       href: articles/alignment-to-external-dataset.html
+  - text: News 
+    href: news/index.html
 structure:
   right:
   - search

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

@@ -13,6 +13,8 @@ vignette: >
 ---
 
 ```{r setup, include=FALSE}
+library(knitr)
+library(quarto)
 knitr::opts_knit$set(root.dir = './')
 ```
 
@@ -27,7 +29,7 @@ packages could be used for different steps and some examples are mentioned
 throughout the workflow.
 
 ![Steps of the end-to-end workflow and possible
-alternatives](\images\workflow.png)
+alternatives](\vignettes\images\workflow.png)
 
 # Data description
 
@@ -42,7 +44,6 @@ Our workflow is therefore based on the following dependencies:
 
 ```{r packages used, message=FALSE, warning=FALSE}
 ## General bioconductor package
-library(Biobase)
 library(BiocStyle)
 library(knitr)
 
@@ -76,7 +77,6 @@ library(CompoundDb)    # Access small compound annotation data.
 library(MetaboAnnotation) # Functionality for metabolite annotation.
 ```
 
-
 # Data import
 
 Note that different equipment will generate various file extensions, so a

vignettes/alignment-to-external-dataset.qmd

@@ -11,6 +11,8 @@ vignette: >
 ---
 
 ```{r setup, include=FALSE}
+library(knitr)
+library(quarto)
 knitr::opts_knit$set(root.dir = './')
 ```
 
@@ -36,7 +38,6 @@ library(MsBackendMetaboLights)
 library(xcms)
 library(MsExperiment)
 library(Spectra)
-library(knitr)
 ```
 
 Setting parallel processing to improve the efficiency of the process:

vignettes/dataset-investigation.qmd

@@ -12,6 +12,12 @@ vignette: >
 
 ## In Construction
 
+```{r setup, include=FALSE}
+library(knitr)
+library(quarto)
+knitr::opts_knit$set(root.dir = './')
+```
+
 # Introduction
 
 So, you (or your amazing lab mate) have finally finished the data acquisition,
@@ -65,3 +71,9 @@ separation was achieved using hydrophilic interaction liquid chromatography
     quality.
 -   Compare pool lc-ms and pool lc-ms/ms and show that we have better separation
     on the second run.
+
+```{r}
+getwd()
+list.files()
+list.dirs()
+```