Update the tutorial

jorainer · jorainer · commit 94b34bc651e5 · 2024-02-15T08:53:44.000+01:00
- Adding an additional section on isotope identification.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: xcmsTutorials
 Title: Exploring and Analyzing LC-MS data with Spectra and xcms
-Version: 1.0.4
+Version: 1.1.0
 Authors@R: c(
 	     person(given = "Johannes", family = "Rainer",
 		    email = "Johannes.Rainer@eurac.edu",
@@ -34,7 +34,8 @@ Suggests:
     knitr,
     rmarkdown,
     RColorBrewer,
-    SummarizedExperiment
+    SummarizedExperiment,
+    pheatmap
 URL: https://jorainer.github.io/xcmsTutorials/
 BugReports: https://github.com/jorainer/xcmsTutorials/issues/new
 VignetteBuilder: knitr
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM bioconductor/bioconductor_docker:RELEASE_3_18
+FROM bioconductor/bioconductor_docker:devel
 
 LABEL name="jorainer/xcms_tutorials" \
       url="https://github.com/jorainer/xcmsTutorials" \
diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,14 @@
 # xcmsTutorials 1.0
 
+## Changes in 1.1.0
+
+- Use Bioconductor 3.19 devel release.
+- Add examples for simple quality assessment of BPC or BPS data.
+- Introduce parameter `ppm` for `PeakDensityParam` correspondence analysis
+  method.
+- Add an additional section for extraction of chromatographic or spectra data
+  for identified chromatographic peaks and perform isotopologue search in these.
+
 ## Changes in 1.0.4
 
 - Use the Bioconductor 3.18 release docker image.
diff --git a/README.md b/README.md
@@ -9,12 +9,12 @@
 ![MsCoreUtils](man/figures/MsCoreUtils.png)
 
 This workshop provides an overview of recent developments in Bioconductor to
-work with mass spectrometry
+work with mass spectrometry data
 ([MsExperiment](https://github.com/RforMassSpectrometry/MsExperiment),
 [Spectra](https://github.com/RforMassSpectrometry/Spectra)) and specifically
 LC-MS data ([xcms](https://github.com/sneumann/xcms)) and walks through the
 preprocessing of a small data set emphasizing on selection of data-dependent
-settings for the individual pre-processing steps.
+settings for the individual preprocessing steps.
 
 Covered topics are:
 
@@ -45,9 +45,12 @@ generate the html file
 
 ## Installation
 
-For on-line code evaluation, the workshop can also be run using a self-contained
-docker image with all R packages and a server version of RStudio (Posit)
-pre-installed:
+The workshop files along with an R runtime environment including all required
+packages and the RStudio (Posit) editor are all bundled in a *docker*
+container. After installation, this docker container can be run on the computer
+and the code and examples from the workshop can be evaluated within this
+environment (without the need to install any additional packages or files). The
+required steps for installation are:
 
 - If you don't already have, install [docker](https://www.docker.com/). Find
   installation information [here](https://docs.docker.com/desktop/).
@@ -59,12 +62,12 @@ pre-installed:
       -e PASSWORD=bioc \
       -p 8787:8787 \
       jorainer/xcms_tutorials:latest
-  ```
+```
 
 - Enter `http://localhost:8787` in a web browser and log in with username
   `rstudio` and password `bioc`.
 - In the RStudio server version: open any of the R-markdown (*.Rmd*) files in
-  the *vignettes* folder and evaluate the R code blocks.
+  the *vignettes* folder and evaluate the R code blocks in that document.
 
 
 For manual installation, an R version >= 4.3.0 is required as well as recent
@@ -103,3 +106,8 @@ Conduct](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/Rf
   https://rformassspectrometry.github.io/MetaboAnnotation/
 - Repository of the `CompoundDb` package:
   https://rformassspectrometry.github.io/CompoundDb/
+
+# Acknowledgments
+
+Thank you to [Philippine Louail](https://github.com/philouail) for fixing typos
+and suggesting improvements.
diff --git a/vignettes/xcms-preprocessing.Rmd b/vignettes/xcms-preprocessing.Rmd

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-FROM bioconductor/bioconductor_docker:RELEASE_3_18`
	`1`	`+FROM bioconductor/bioconductor_docker:devel`
`2`	`2`
`3`	`3`	`LABEL name="jorainer/xcms_tutorials" \`
`4`	`4`	`url="https://github.com/jorainer/xcmsTutorials" \`