diff --git a/Dockerfile b/Dockerfile index 2ac0117..2f9e7ae 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,6 +11,6 @@ WORKDIR /home/rstudio COPY --chown=rstudio:rstudio . /home/rstudio/ ## Install the xcmsTutorials package and additional required packages -RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask = FALSE); BiocManager::install('sneumann/xcms')" +RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask = FALSE); BiocManager::install('sneumann/xcms', ref = 'jomain')" RUN Rscript -e "options(repos = c(CRAN = 'https://cran.r-project.org')); devtools::install('.', dependencies = TRUE, build_vignettes = TRUE, repos = BiocManager::repositories())" diff --git a/vignettes/xcms-preprocessing.Rmd b/vignettes/xcms-preprocessing.Rmd index 1f2a52a..75ea0b3 100644 --- a/vignettes/xcms-preprocessing.Rmd +++ b/vignettes/xcms-preprocessing.Rmd @@ -46,7 +46,8 @@ which is followed by the description of a simple data centroiding approach and finally we present an *xcms*-based LC-MS data preprocessing that comprises chromatographic peak detection, alignment and correspondence. Data normalization procedures, compound identification and differential abundance analysis are not -covered here. Particular emphasis is given on deriving and defining data set-dependent values for the most critical *xcms* preprocessing parameters. +covered here. Particular emphasis is given on deriving and defining data +set-dependent values for the most critical *xcms* preprocessing parameters. # Introduction