Update Links

R/calculate_protein_abundance.R

@@ -22,7 +22,7 @@
 #' intensities as the protein abundance. Another option is `"iq"`, which performs protein
 #' quantification based on a maximal peptide ratio extraction algorithm that is adapted from the
 #' MaxLFQ algorithm of the MaxQuant software. Functions from the
-#' \href{https://doi.org/10.1093/bioinformatics/btz961}{`iq`} package are
+#' \href{https://academic.oup.com/bioinformatics/article/36/8/2611/5697917}{`iq`} package are
 #' used. Default is `"iq"`.
 #' @param for_plot a logical value indicating whether the result should be only protein intensities
 #' or protein intensities together with precursor intensities that can be used for plotting using

R/data.R

@@ -25,7 +25,7 @@
 #' Rapamycin 10 uM example data
 #'
 #' Rapamycin example data used for the vignette about binary control/treated data. The data was
-#' obtained from \href{https://doi.org/10.1038/s41467-020-18071-x}{Piazza 2020}
+#' obtained from \href{https://www.nature.com/articles/s41467-020-18071-x}{Piazza 2020}
 #' and corresponds to experiment 18. FKBP1A the rapamycin binding protein and 49 other randomly
 #' sampled proteins were used for this example dataset. Furthermore, only the DMSO control and the
 #' 10 uM condition were used.
@@ -39,7 +39,7 @@
 #' Rapamycin dose response example data
 #'
 #' Rapamycin example data used for the vignette about dose response data. The data was obtained
-#' from \href{https://doi.org/10.1038/s41467-020-18071-x}{Piazza 2020} and corresponds
+#' from \href{https://www.nature.com/articles/s41467-020-18071-x}{Piazza 2020} and corresponds
 #' to experiment 18. FKBP1A the rapamycin binding protein and 39 other randomly sampled proteins
 #' were used for this example dataset. The concentration range includes the following points:
 #' 0 (DMSO control), 10 pM, 100 pM, 1 nM, 10 nM, 100 nM, 1 uM, 10 uM and 100 uM.

R/fetch_eco.R

@@ -19,7 +19,7 @@
 #' information."
 #'
 #' More information can be found in their
-#' \href{https://doi.org/10.1093/nar/gky1036}{publication}.
+#' \href{https://academic.oup.com/nar/article/47/D1/D1186/5165344}{publication}.
 #'
 #' @param return_relation a logical value that indicates if relational information should be returned instead
 #' the main descriptive information. This data can be used to check the relations of ECO terms to each other.