diff --git a/man/CCAIntegration.Rd b/man/CCAIntegration.Rd
index b8399ad04..f4f1e5b0a 100644
--- a/man/CCAIntegration.Rd
+++ b/man/CCAIntegration.Rd
@@ -33,7 +33,7 @@ CCAIntegration(
 
 \item{layers}{Names of layers in \code{assay}}
 
-\item{orig}{A \link[SeuratObject:DimReduc]{dimensional reduction} to correct}
+\item{orig}{A \link[SeuratObject]{DimReduc} to correct}
 
 \item{new.reduction}{Name of new integrated dimensional reduction}
 
@@ -61,7 +61,7 @@ weights. This can be one of:
    all objects to be integrated}
    \item{A vector of strings, specifying the name of a dimension reduction to
    use for each object to be integrated}
-   \item{A vector of \code{\link{DimReduc}} objects, specifying the object to
+   \item{A vector of \code{\link[SeuratObject]{DimReduc}} objects, specifying the object to
    use for each object in the integration}
    \item{NULL, in which case the full corrected space is used for computing
    anchor weights.}
diff --git a/man/FindNeighbors.Rd b/man/FindNeighbors.Rd
index 0c4b8c703..de80c0ab5 100644
--- a/man/FindNeighbors.Rd
+++ b/man/FindNeighbors.Rd
@@ -98,7 +98,7 @@ be set automatically}
 
 \item{k.param}{Defines k for the k-nearest neighbor algorithm}
 
-\item{return.neighbor}{Return result as \code{\link{Neighbor}} object. Not
+\item{return.neighbor}{Return result as \code{\link[SeuratObject]{Neighbor}} object. Not
 used with distance matrix input.}
 
 \item{compute.SNN}{also compute the shared nearest neighbor graph}
@@ -152,13 +152,13 @@ neighbor (NN) graph, and the second element used to store the SNN graph. If
 only one name is supplied, only the NN graph is stored.}
 }
 \value{
-This function can either return a \code{\link{Neighbor}} object
-with the KNN information or a list of \code{\link{Graph}} objects with
+This function can either return a \code{\link[SeuratObject]{Neighbor}} object
+with the KNN information or a list of \code{\link[SeuratObject]{Graph}} objects with
 the KNN and SNN depending on the settings of \code{return.neighbor} and
-\code{compute.SNN}. When running on a \code{\link{Seurat}} object, this
-returns the \code{\link{Seurat}} object with the Graphs or Neighbor objects
+\code{compute.SNN}. When running on a \code{\link[SeuratObject]{Seurat}} object, this
+returns the \code{\link[SeuratObject]{Seurat}} object with the Graphs or Neighbor objects
 stored in their respective slots. Names of the Graph or Neighbor object can
-be found with \code{\link{Graphs}} or \code{\link{Neighbors}}.
+be found with \code{\link[SeuratObject]{Graphs}} or \code{\link[SeuratObject]{Neighbors}}.
 }
 \description{
 Computes the \code{k.param} nearest neighbors for a given dataset. Can also
diff --git a/man/FindTransferAnchors.Rd b/man/FindTransferAnchors.Rd
index f0dfbbc60..4ea81c058 100644
--- a/man/FindTransferAnchors.Rd
+++ b/man/FindTransferAnchors.Rd
@@ -33,9 +33,9 @@ FindTransferAnchors(
 )
 }
 \arguments{
-\item{reference}{\code{\link{Seurat}} object to use as the reference}
+\item{reference}{\code{\link[SeuratObject]{Seurat}} object to use as the reference}
 
-\item{query}{\code{\link{Seurat}} object to use as the query}
+\item{query}{\code{\link[SeuratObject]{Seurat}} object to use as the query}
 
 \item{normalization.method}{Name of normalization method used: LogNormalize
 or SCT.}
@@ -109,7 +109,7 @@ annoy}
 nearest neighbor search}
 
 \item{eps}{Error bound on the neighbor finding algorithm (from
-\code{\link{RANN}} or \code{\link{RcppAnnoy}})}
+\code{\link[RANN]{RANN}} or \code{\link[RcppAnnoy]{RcppAnnoy}})}
 
 \item{approx.pca}{Use truncated singular value decomposition to approximate
 PCA}
diff --git a/man/IntegrateData.Rd b/man/IntegrateData.Rd
index e08bd682e..399fdc3fc 100644
--- a/man/IntegrateData.Rd
+++ b/man/IntegrateData.Rd
@@ -47,8 +47,8 @@ weights. This can be one of:
 all objects to be integrated}
 \item{A vector of strings, specifying the name of a dimension reduction to
 use for each object to be integrated}
-\item{A vector of \code{\link{DimReduc}} objects, specifying the object to
-use for each object in the integration}
+\item{A vector of \code{\link[SeuratObject]{DimReduc}} objects,
+specifying the object to use for each object in the integration}
 \item{NULL, in which case a new PCA will be calculated and used to
 calculate anchor weights}
 }
@@ -80,13 +80,13 @@ If NULL, the sample tree will be computed automatically.}
 integration.}
 
 \item{eps}{Error bound on the neighbor finding algorithm (from
-\code{\link{RANN}})}
+\code{\link[RANN]{RANN}})}
 
 \item{verbose}{Print progress bars and output}
 }
 \value{
-Returns a \code{\link{Seurat}} object with a new integrated
-\code{\link{Assay}}. If \code{normalization.method = "LogNormalize"}, the
+Returns a \code{\link[SeuratObject]{Seurat}} object with a new integrated
+\code{\link[SeuratObject]{Assay}}. If \code{normalization.method = "LogNormalize"}, the
 integrated data is returned to the \code{data} slot and can be treated as
 log-normalized, corrected data. If \code{normalization.method = "SCT"}, the
 integrated data is returned to the \code{scale.data} slot and can be treated
diff --git a/man/IntegrateEmbeddings.Rd b/man/IntegrateEmbeddings.Rd
index 304d0500a..61a185f92 100644
--- a/man/IntegrateEmbeddings.Rd
+++ b/man/IntegrateEmbeddings.Rd
@@ -49,7 +49,7 @@ IntegrateEmbeddings(anchorset, ...)
 \item{reductions}{Name of reductions to be integrated. For a
 TransferAnchorSet, this should be the name of a reduction present in the
 anchorset object (for example, "pcaproject"). For an IntegrationAnchorSet,
-this should be a \code{\link{DimReduc}} object containing all cells present
+this should be a \code{\link[SeuratObject]{DimReduc}} object containing all cells present
 in the anchorset object.}
 
 \item{dims.to.integrate}{Number of dimensions to return integrated values for}
@@ -63,7 +63,7 @@ weights. This can be one of:
    all objects to be integrated}
    \item{A vector of strings, specifying the name of a dimension reduction to
    use for each object to be integrated}
-   \item{A vector of \code{\link{DimReduc}} objects, specifying the object to
+   \item{A vector of \code{\link[SeuratObject]{DimReduc}} objects, specifying the object to
    use for each object in the integration}
    \item{NULL, in which case the full corrected space is used for computing
    anchor weights.}
diff --git a/man/JointPCAIntegration.Rd b/man/JointPCAIntegration.Rd
index 3f2ab73f7..a390c1f23 100644
--- a/man/JointPCAIntegration.Rd
+++ b/man/JointPCAIntegration.Rd
@@ -33,7 +33,7 @@ JointPCAIntegration(
 
 \item{layers}{Names of layers in \code{assay}}
 
-\item{orig}{A \link[SeuratObject:DimReduc]{dimensional reduction} to correct}
+\item{orig}{A \link[SeuratObject]{DimReduc} to correct}
 
 \item{new.reduction}{Name of new integrated dimensional reduction}
 
@@ -61,7 +61,7 @@ weights. This can be one of:
    all objects to be integrated}
    \item{A vector of strings, specifying the name of a dimension reduction to
    use for each object to be integrated}
-   \item{A vector of \code{\link{DimReduc}} objects, specifying the object to
+   \item{A vector of \code{\link[SeuratObject]{DimReduc}} objects, specifying the object to
    use for each object in the integration}
    \item{NULL, in which case the full corrected space is used for computing
    anchor weights.}
diff --git a/man/PrepSCTIntegration.Rd b/man/PrepSCTIntegration.Rd
index d3fdecae4..8052e10e2 100644
--- a/man/PrepSCTIntegration.Rd
+++ b/man/PrepSCTIntegration.Rd
@@ -13,11 +13,11 @@ PrepSCTIntegration(
 )
 }
 \arguments{
-\item{object.list}{A list of \code{\link{Seurat}} objects to prepare for integration}
+\item{object.list}{A list of \code{\link[SeuratObject]{Seurat}} objects to prepare for integration}
 
-\item{assay}{The name of the \code{\link{Assay}} to use for integration. This can be a
+\item{assay}{The name of the \code{\link[SeuratObject]{Assay}} to use for integration. This can be a
 single name if all the assays to be integrated have the same name, or a character vector
-containing the name of each \code{\link{Assay}} in each object to be integrated. The
+containing the name of each \code{\link[SeuratObject]{Assay}} in each object to be integrated. The
 specified assays must have been normalized using \code{\link{SCTransform}}.
 If NULL (default), the current default assay for each object is used.}
 
@@ -35,7 +35,7 @@ the Pearson residual will be clipped to}
 \item{verbose}{Display output/messages}
 }
 \value{
-A list of \code{\link{Seurat}} objects with the appropriate \code{scale.data} slots
+A list of \code{\link[SeuratObject]{Seurat}} objects with the appropriate \code{scale.data} slots
 containing only the required \code{anchor.features}.
 }
 \description{
diff --git a/man/RPCAIntegration.Rd b/man/RPCAIntegration.Rd
index 0e4589d68..3c93933c2 100644
--- a/man/RPCAIntegration.Rd
+++ b/man/RPCAIntegration.Rd
@@ -33,7 +33,7 @@ RPCAIntegration(
 
 \item{layers}{Names of layers in \code{assay}}
 
-\item{orig}{A \link[SeuratObject:DimReduc]{dimensional reduction} to correct}
+\item{orig}{A \link[SeuratObject]{DimReduc} to correct}
 
 \item{new.reduction}{Name of new integrated dimensional reduction}
 
@@ -61,7 +61,7 @@ weights. This can be one of:
    all objects to be integrated}
    \item{A vector of strings, specifying the name of a dimension reduction to
    use for each object to be integrated}
-   \item{A vector of \code{\link{DimReduc}} objects, specifying the object to
+   \item{A vector of \code{\link[SeuratObject]{DimReduc}} objects, specifying the object to
    use for each object in the integration}
    \item{NULL, in which case the full corrected space is used for computing
    anchor weights.}
diff --git a/man/RunCCA.Rd b/man/RunCCA.Rd
index aa2c6b14b..71091ba23 100644
--- a/man/RunCCA.Rd
+++ b/man/RunCCA.Rd
@@ -91,6 +91,6 @@ print(x = pbmc_cca[["cca"]])
 
 }
 \seealso{
-\code{\link{merge.Seurat}}
+\code{\link[SeuratObject]{merge.Seurat}}
 }
 \concept{dimensional_reduction}
diff --git a/man/RunSPCA.Rd b/man/RunSPCA.Rd
index 11c23986e..87fb7efa3 100644
--- a/man/RunSPCA.Rd
+++ b/man/RunSPCA.Rd
@@ -99,6 +99,6 @@ matrix factorization.
 Barshan E, Ghodsi A, Azimifar Z, Jahromi MZ.
 Supervised principal component analysis: Visualization, classification and
 regression on subspaces and submanifolds.
-Pattern Recognition. 2011 Jul 1;44(7):1357-71. \url{https://www.sciencedirect.com/science/article/pii/S0031320310005819?casa_token=AZMFg5OtPnAAAAAA:_Udu7GJ7G2ed1-XSmr-3IGSISUwcHfMpNtCj-qacXH5SBC4nwzVid36GXI3r8XG8dK5WOQui};
+Pattern Recognition. 2011 Jul 1;44(7):1357-71. \url{doi:10.1016/j.patcog.2010.12.015};
 }
 \concept{dimensional_reduction}
diff --git a/man/SCTAssay-class.Rd b/man/SCTAssay-class.Rd
index d116a62e9..5feba288a 100644
--- a/man/SCTAssay-class.Rd
+++ b/man/SCTAssay-class.Rd
@@ -27,7 +27,7 @@
 The SCTModel object is a model and parameters storage from SCTransform.
 It can be used to calculate Pearson residuals for new genes.
 
-The SCTAssay object contains all the information found in an \code{\link{Assay}}
+The SCTAssay object contains all the information found in an \code{\link[SeuratObject]{Assay}}
 object, with extra information from the results of \code{\link{SCTransform}}
 }
 \section{Slots}{
@@ -93,8 +93,8 @@ levels(pbmc_small[['SCT']])
 
 }
 \seealso{
-\code{\link{Assay}}
+\code{\link[SeuratObject]{Assay}}
 
-\code{\link{Assay}}
+\code{\link[SeuratObject]{Assay}}
 }
 \concept{objects}
diff --git a/man/TopNeighbors.Rd b/man/TopNeighbors.Rd
index 64dc5cc67..1c029803a 100644
--- a/man/TopNeighbors.Rd
+++ b/man/TopNeighbors.Rd
@@ -7,7 +7,7 @@
 TopNeighbors(object, cell, n = 5)
 }
 \arguments{
-\item{object}{\code{\link{Neighbor}} object}
+\item{object}{\code{\link[SeuratObject]{Neighbor}} object}
 
 \item{cell}{Cell of interest}
 
diff --git a/man/TransferData.Rd b/man/TransferData.Rd
index e30977df7..4df588c51 100644
--- a/man/TransferData.Rd
+++ b/man/TransferData.Rd
@@ -53,7 +53,7 @@ anchors. Options are:
    \item{lsiproject: Use the projected LSI used for anchor building}
    \item{pca: Use an internal PCA on the query only}
    \item{cca: Use the CCA used for anchor building}
-   \item{custom DimReduc: User provided \code{\link{DimReduc}} object
+   \item{custom DimReduc: User provided \code{\[SeuratObject]{DimReduc}} object
    computed on the query cells}
 }}
 
@@ -69,7 +69,7 @@ weighting.}
 \item{sd.weight}{Controls the bandwidth of the Gaussian kernel for weighting}
 
 \item{eps}{Error bound on the neighbor finding algorithm (from
-\code{\link{RANN}})}
+\code{\link[RANN]{RANN}})}
 
 \item{n.trees}{More trees gives higher precision when using annoy approximate
 nearest neighbor search}
diff --git a/man/fortify-Spatial.Rd b/man/fortify-Spatial.Rd
index e2d13bcf8..b19fea1b6 100644
--- a/man/fortify-Spatial.Rd
+++ b/man/fortify-Spatial.Rd
@@ -15,9 +15,9 @@
 \method{fortify}{Segmentation}(model, data, ...)
 }
 \arguments{
-\item{model}{A \code{\linkS4class{Segmentation}},
-\code{\linkS4class{Centroids}},
-or \code{\linkS4class{Molecules}} object}
+\item{model}{A \code{\link[SeuratObject:Segmentation-class]{Segmentation}},
+\code{\link[SeuratObject:Centroids-class]{Centroids}},
+or \code{\link[SeuratObject:Molecules-class]{Molecules}} object}
 
 \item{data}{Extra data to be used for annotating the cell segmentations; the
 easiest way to pass data is a one-column