diff --git a/DESCRIPTION b/DESCRIPTION
index 36df187b1..5309c9024 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -85,6 +85,7 @@ Imports:
     tidyr,
     utils,
     vegan,
+    Rdpack,
     Rcpp
 Suggests:
     ade4,
@@ -114,3 +115,4 @@ BugReports: https://github.com/microbiome/mia/issues
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
 VignetteBuilder: knitr
+RdMacros: Rdpack
diff --git a/R/addLDA.R b/R/addLDA.R
index f512c3dfd..8798887cd 100644
--- a/R/addLDA.R
+++ b/R/addLDA.R
@@ -40,6 +40,9 @@
 #' \code{\link[topicmodels:LDA]{LDA}} to compute the ordination matrix and
 #' feature loadings.
 #'
+#' @references
+#' \insertRef{Blei2003}{mia}
+#'
 #' @name addLDA
 #'
 #' @examples
diff --git a/R/addNMF.R b/R/addNMF.R
index 820efb752..58244b749 100644
--- a/R/addNMF.R
+++ b/R/addNMF.R
@@ -55,6 +55,9 @@
 #' values contained in k, and the best fit is selected based on
 #' \code{eval.metric} value.
 #'
+#' @references
+#' \insertRef{Brunet2004}{mia}
+#'
 #' @name addNMF
 #'
 #' @examples
diff --git a/R/calculateDMM.R b/R/calculateDMM.R
index 4fe554218..813153a88 100644
--- a/R/calculateDMM.R
+++ b/R/calculateDMM.R
@@ -59,6 +59,9 @@
 #' \code{\link[DirichletMultinomial:cvdmngroup]{cvdmngroup }},
 #' \code{\link[DirichletMultinomial:fitted]{accessors for DMN objects}}
 #'
+#' @references
+#' \insertRef{Holmes2012}{mia}
+#'
 #' @name calculateDMN
 #'
 #' @examples
diff --git a/R/getPERMANOVA.R b/R/getPERMANOVA.R
index 7c5a5c786..f6ed952de 100644
--- a/R/getPERMANOVA.R
+++ b/R/getPERMANOVA.R
@@ -112,6 +112,9 @@
 #' \code{\link[vegan:permutest]{vegan::permutest}}. See also
 #' \code{\link[=runCCA]{addCCA}} and \code{\link[=runCCA]{addRDA}}
 #'
+#' @references
+#' \insertRef{Anderson2001}{mia}
+#'
 NULL
 
 #' @export
diff --git a/R/runDPCoA.R b/R/runDPCoA.R
index 6ca945ef7..50c51754f 100644
--- a/R/runDPCoA.R
+++ b/R/runDPCoA.R
@@ -68,6 +68,9 @@
 #' \code{\link[scater:plotReducedDim]{plotReducedDim}}
 #' \code{\link[SingleCellExperiment:reducedDims]{reducedDims}}
 #'
+#' @references
+#' \insertRef{Pavoine2004}{mia}
+#'
 #' @examples
 #' data(esophagus)
 #' dpcoa <- getDPCoA(esophagus)
diff --git a/R/runNMDS.R b/R/runNMDS.R
index 2c0b96f3b..079ccf9e3 100644
--- a/R/runNMDS.R
+++ b/R/runNMDS.R
@@ -62,6 +62,9 @@
 #' \code{\link[scater:plotReducedDim]{plotMDS}}, to quickly visualize the
 #' results.
 #'
+#' @references
+#' \insertRef{Kruskal1964}{mia}
+#'
 #' @examples
 #' # generate some example data
 #' mat <- matrix(1:60, nrow = 6)
diff --git a/inst/REFERENCES.bib b/inst/REFERENCES.bib
new file mode 100644
index 000000000..3c74ff23c
--- /dev/null
+++ b/inst/REFERENCES.bib
@@ -0,0 +1,74 @@
+@article{Holmes2012,
+  author  = {Ian Holmes and Katherine Harris and Christopher Quince},
+  title   = {Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics},
+  journal = {PLOS ONE},
+  year    = {2012},
+  volume  = {7},
+  number  = {2},
+  pages   = {e30126},
+  doi     = {10.1371/journal.pone.0030126}
+}
+
+@article{Blei2003,
+  author  = {David M. Blei and Andrew Y. Ng and Michael I. Jordan},
+  title   = {Latent Dirichlet Allocation},
+  journal = {Journal of Machine Learning Research},
+  year    = {2003},
+  volume  = {3},
+  pages   = {993--1022}
+}
+
+@article{Brunet2004,
+  author  = {Jean-Philippe Brunet and Pablo Tamayo and Todd R. Golub and Jill P. Mesirov},
+  title   = {Metagenes and Molecular Pattern Discovery Using Matrix Factorization},
+  journal = {Proceedings of the National Academy of Sciences},
+  year    = {2004},
+  volume  = {101},
+  number  = {12},
+  pages   = {4164--4169},
+  doi     = {10.1073/pnas.0308531101}
+}
+
+@article{Kruskal1964,
+  author  = {Joseph B. Kruskal},
+  title   = {Nonmetric Multidimensional Scaling: A Numerical Method},
+  journal = {Psychometrika},
+  year    = {1964},
+  volume  = {29},
+  number  = {2},
+  pages   = {115--129},
+  doi     = {10.1007/BF02289694}
+}
+
+@article{Pavoine2004,
+  author  = {Sandrine Pavoine and Jean Vallet and Anne-B{\'e}atrice Dufour and Stella Gachet and Daniel Daniel Schmitt},
+  title   = {Dissimilarity Measurements and Ordinations for Ecological Data: An Example Using {DPCoA}},
+  journal = {Ecology},
+  year    = {2004},
+  volume  = {85},
+  number  = {2},
+  pages   = {280--288},
+  doi     = {10.1890/02-0605}
+}
+
+@article{Anderson2001,
+  author  = {Marti J. Anderson},
+  title   = {A New Method for Non-parametric Multivariate Analysis of Variance},
+  journal = {Austral Ecology},
+  year    = {2001},
+  volume  = {26},
+  number  = {1},
+  pages   = {32--46},
+  doi     = {10.1111/j.1442-9993.2001.01070.pp.x}
+}
+
+@article{Lozupone2005,
+  author  = {Catherine Lozupone and Rob Knight},
+  title   = {UniFrac: A New Phylogenetic Method for Comparing Microbial Communities},
+  journal = {Applied and Environmental Microbiology},
+  year    = {2005},
+  volume  = {71},
+  number  = {12},
+  pages   = {8228--8235},
+  doi     = {10.1128/AEM.71.12.8228-8235.2005}
+}
diff --git a/man/addLDA.Rd b/man/addLDA.Rd
index 8d00adcd0..87bd9836a 100644
--- a/man/addLDA.Rd
+++ b/man/addLDA.Rd
@@ -78,3 +78,6 @@ tab <- getReducedDimAttribute(tse, "LDA_10","eval_metrics")
 # Plot
 plot(tab[["k"]], tab[["perplexity"]], xlab = "k", ylab = "perplexity")
 }
+\references{
+\insertRef{Blei2003}{mia}
+}
diff --git a/man/addNMF.Rd b/man/addNMF.Rd
index 6b292da14..b1885622b 100644
--- a/man/addNMF.Rd
+++ b/man/addNMF.Rd
@@ -101,3 +101,6 @@ loadings_NMF_4 <- getReducedDimAttribute(tse, "NMF_4", "loadings")
 head(loadings_NMF_4)
 
 }
+\references{
+\insertRef{Brunet2004}{mia}
+}
diff --git a/man/calculateDMN.Rd b/man/calculateDMN.Rd
index b0e1e635f..c8590f8a4 100644
--- a/man/calculateDMN.Rd
+++ b/man/calculateDMN.Rd
@@ -180,6 +180,9 @@ head(metadata(tse)$DMM$prob)
 # Get the weight of each component for the best model
 bestModel@mixture$Weight
 }
+\references{
+\insertRef{Holmes2012}{mia}
+}
 \seealso{
 \code{\link[DirichletMultinomial:DMN-class]{DMN-class}},
 \code{\link[DirichletMultinomial:DMNGroup-class]{DMNGroup-class}},
diff --git a/man/getPERMANOVA.Rd b/man/getPERMANOVA.Rd
index ccb3c4574..c11bfdbc9 100644
--- a/man/getPERMANOVA.Rd
+++ b/man/getPERMANOVA.Rd
@@ -140,6 +140,9 @@ rda_res <- getRDA(
 # Significance results are similar to PERMANOVA
 attr(rda_res, "significance")
 
+}
+\references{
+\insertRef{Anderson2001}{mia}
 }
 \seealso{
 For more details on the actual implementation see
diff --git a/man/runDPCoA.Rd b/man/runDPCoA.Rd
index fdd6b627c..6164f7d59 100644
--- a/man/runDPCoA.Rd
+++ b/man/runDPCoA.Rd
@@ -120,6 +120,9 @@ reducedDims(esophagus)
 library(scater)
 plotReducedDim(esophagus, "DPCoA")
 }
+\references{
+\insertRef{Pavoine2004}{mia}
+}
 \seealso{
 \code{\link[scater:plotReducedDim]{plotReducedDim}}
 \code{\link[SingleCellExperiment:reducedDims]{reducedDims}}
diff --git a/man/runNMDS.Rd b/man/runNMDS.Rd
index 66f2c228a..334213cb7 100644
--- a/man/runNMDS.Rd
+++ b/man/runNMDS.Rd
@@ -152,6 +152,9 @@ esophagus <- addNMDS(esophagus, FUN = vegan::vegdist, name = "euclidean",
                      method = "euclidean")
 reducedDims(esophagus)
 }
+\references{
+\insertRef{Kruskal1964}{mia}
+}
 \seealso{
 \code{\link[MASS:isoMDS]{MASS::isoMDS}},
 \code{\link[vegan:monoMDS]{vegan::monoMDS}}