@@ -52,7 +52,7 @@

 #'

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with

 #'  'decontX_Contamination' and 'decontX_Clusters' added to the

-#'  \link[SummarizedExperiment]{colData} slot. Additionally, the

+#'  \link{colData} slot. Additionally, the

 #' decontaminated counts will be added as an assay called 'decontXCounts'.

 #' @examples

 #' data(scExample, package = "singleCellTK")

@@ -46,7 +46,7 @@

 #' @param df See \link[DropletUtils]{emptyDrops} for more information. Default \code{20}.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with the

 #'  \link[DropletUtils]{barcodeRanks} output table appended to the

-#'  \link[SummarizedExperiment]{colData} slot. The columns include

+#'  \link{colData} slot. The columns include

 #'  \emph{dropletUtils_BarcodeRank_Knee} and \emph{dropletUtils_BarcodeRank_Knee}

 #'  Please refer to the documentation of \link[DropletUtils]{barcodeRanks} for

 #'  details.

@@ -45,7 +45,7 @@

 #' @param BPPARAM See \link[DropletUtils]{emptyDrops} for more information.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with the

 #'  \link[DropletUtils]{emptyDrops} output table appended to the

-#'  \link[SummarizedExperiment]{colData} slot. The columns include

+#'  \link{colData} slot. The columns include

 #'  \emph{emptyDrops_total}, \emph{emptyDrops_logprob},

 #'  \emph{emptyDrops_pvalue}, \emph{emptyDrops_limited}, \emph{emptyDrops_fdr}.

 #'  Please refer to the documentation of \link[DropletUtils]{emptyDrops} for

@@ -6,20 +6,20 @@

 #' @param inSCE A \code{\link[SingleCellExperiment]{SingleCellExperiment}}

 #' object.

 #' @param useAssay A single \code{character}, specifying which

-#' \code{\link[SummarizedExperiment]{assay}} to perform the clustering algorithm

+#' \code{\link{assay}} to perform the clustering algorithm

 #' on. Default \code{NULL}.

 #' @param useReducedDim A single \code{character}, specifying which

-#' low-dimension representation (\code{\link[SingleCellExperiment]{reducedDim}})

+#' low-dimension representation (\code{\link{reducedDim}})

 #' to perform the clustering algorithm on. Default \code{NULL}.

 #' @param useAltExp A single \code{character}, specifying the assay which

-#' \code{\link[SingleCellExperiment]{altExp}} to perform the clustering

+#' \code{\link{altExp}} to perform the clustering

 #' algorithm on. Default \code{NULL}.

 #' @param altExpAssay A single \code{character}, specifying which

-#' \code{\link[SummarizedExperiment]{assay}} in the chosen

-#' \code{\link[SingleCellExperiment]{altExp}} to work on. Only used when

+#' \code{\link{assay}} in the chosen

+#' \code{\link{altExp}} to work on. Only used when

 #' \code{useAltExp} is set. Default \code{"counts"}.

 #' @param clusterName A single \code{character}, specifying the name to store

-#' the cluster label in \code{\link[SummarizedExperiment]{colData}}. Default

+#' the cluster label in \code{\link{colData}}. Default

 #' \code{"scranSNN_cluster"}.

 #' @param k An \code{integer}, the number of nearest neighbors used to construct

 #' the graph. Smaller value indicates higher resolution and larger number of

@@ -109,7 +109,7 @@ runScranSNN <- function(inSCE, useAssay = NULL, useReducedDim = NULL,

 #' low-dimension representation to perform the clustering algorithm on. Default

 #' \code{"PCA"}.

 #' @param clusterName A single \code{character}, specifying the name to store

-#' the cluster label in \code{\link[SummarizedExperiment]{colData}}. Default

+#' the cluster label in \code{\link{colData}}. Default

 #' \code{"scranSNN_cluster"}.

 #' @param nCenters An \code{integer}, the number of centroids (clusters).

 #' @param nIter An \code{integer}, the maximum number of iterations allowed.

@@ -9,11 +9,11 @@

 #' selected.variable features. Default \code{NULL}.

 #' @param sample Character vector. Indicates which sample each cell belongs to.

 #' If given a single character, will take the annotation from

-#' \code{\link[SummarizedExperiment]{colData}}. Default \code{NULL}.

+#' \code{\link{colData}}. Default \code{NULL}.

 #' @param reducedDimName A name to store the results of the dimension reduction

 #' coordinates obtained from this method. Default \code{"UMAP"}.

 #' @param logNorm Whether the counts will need to be log-normalized prior to

-#' generating the UMAP via \code{\link[scater]{logNormCounts}}. Default

+#' generating the UMAP via \code{\link{logNormCounts}}. Default

 #' \code{TRUE}.

 #' @param nNeighbors The size of local neighborhood used for manifold

 #' approximation. Larger values result in more global views of the manifold,

@@ -29,7 +29,7 @@

 #' result on a more even dispersal of points. Default \code{0.01}. See

 #' `?uwot::umap` for more information.

 #' @param spread The effective scale of embedded points. In combination with

-#' ‘min_dist’, this determines how clustered/clumped the embedded points are.

+#' minDist, this determines how clustered/clumped the embedded points are.

 #' Default \code{1}. See `?uwot::umap` for more information.

 #' @param pca Logical. Whether to perform dimension reduction with PCA before

 #' UMAP. Default \code{TRUE}

@@ -83,7 +83,7 @@

 #'   with the sample name appended to each colname in colData

 #' }

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object. Default \code{TRUE}.

+#'  \link{DelayedArray} object. Default \code{TRUE}.

 #' @details

 #' \code{importAnnData} converts scRNA-seq data in the AnnData format to the

 #' \code{SingleCellExperiment} object. The .X slot in AnnData is transposed to the features x cells

@@ -99,10 +99,10 @@

 #'  \code{samples}.

 #' @param class Character. The class of the expression matrix stored in the SCE

 #'  object. Can be one of "Matrix" (as returned by

-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by

+#'  \link{readMM} function), or "matrix" (as returned by

 #'  \link[base]{matrix} function). Default "Matrix".

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link[DelayedArray]{DelayedArray-class} object or not. Default \code{TRUE}.

 #' @return A \code{SingleCellExperiment} object containing the count

 #'  matrix, the gene annotation, and the cell annotation.

 #' @examples

@@ -433,7 +433,7 @@

 #' \itemize{

 #'   \item \code{NULL}. All samples within \code{cellRangerDirs} will be

 #'    imported. The order of samples will be first determined by the order of

-#'    \code{cellRangerDirs} and then by \link[base]{list.dirs}. This is only

+#'    \code{cellRangerDirs} and then by \link{list.dirs}. This is only

 #'    for the case where \code{cellRangerDirs} is specified.

 #'   \item A list of vectors containing the folder names for samples to import.

 #'    Each vector in

@@ -509,10 +509,10 @@

 #'  \code{unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE))}.

 #' @param class Character. The class of the expression matrix stored in the SCE

 #'  object. Can be one of "Matrix" (as returned by

-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by

+#'  \link{readMM} function), or "matrix" (as returned by

 #'  \link[base]{matrix} function). Default \code{"Matrix"}.

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link{DelayedArray} object or not. Default \code{TRUE}.

 #' @param reference Character vector. The reference genome names. 

 #'  Default \code{NULL}. If not \code{NULL}, it must gave the length and order as 

 #'  \code{length(unlist(sampleDirs))} if \code{sampleDirs} is not \code{NULL}.

@@ -653,10 +653,10 @@ importCellRangerV2 <- function(

 #'  Default "sample".

 #' @param class Character. The class of the expression matrix stored in the SCE

 #'  object. Can be one of "Matrix" (as returned by

-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by

+#'  \link{readMM} function), or "matrix" (as returned by

 #'  \link[base]{matrix} function). Default "Matrix".

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link{DelayedArray} object or not. Default \code{TRUE}.

 #' @return A \code{SingleCellExperiment} object containing the count

 #'  matrix, the feature annotations, and the cell annotation for the sample.

 #' @examples

@@ -737,10 +737,10 @@ importCellRangerV3 <- function(

 #'  Default "sample".

 #' @param class Character. The class of the expression matrix stored in the SCE

 #'  object. Can be one of "Matrix" (as returned by

-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by

+#'  \link{readMM} function), or "matrix" (as returned by

 #'  \link[base]{matrix} function). Default "Matrix".

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link{DelayedArray} object or not. Default \code{TRUE}.

 #' @return A \code{SingleCellExperiment} object containing the count

 #'  matrix, the feature annotations, and the cell annotation for the sample.

 #' @examples

@@ -91,7 +91,7 @@

 #' @param dataType can be "filtered" or "raw". Default \code{"filtered"}.

 #' @param rdsFileName File name prefix of the DropEst RDS output. default is "cell.counts"

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link{DelayedArray} object or not. Default \code{TRUE}.

 #' @details

 #' \code{importDropEst} expects either raw counts matrix stored as "cm_raw" or filtered

 #' counts matrix stored as "cm" in the DropEst rds output.

@@ -2,7 +2,7 @@

 #' @title Retrieve example datasets

 #' @description Retrieves published example datasets stored in

 #' \link[SingleCellExperiment]{SingleCellExperiment} using the

-#' \link[scRNAseq]{scRNAseq} and

+#' \link{scRNAseq} and

 #' \link[TENxPBMCData]{TENxPBMCData} packages. See 'Details' for a

 #' list of available datasets.

 #' @param dataset Character. Name of the dataset to retrieve.

@@ -12,16 +12,16 @@

 #'   \code{"matrix"} will store the data in a standard matrix. Default

 #'   \code{"Matrix"}.

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'   \link[DelayedArray]{DelayedArray} object or not. Default \code{FALSE}.

+#'   \link{DelayedArray} object or not. Default \code{FALSE}.

 #' @details See the list below for the available datasets and their

 #' descriptions.

 #' \describe{

 #' \item{"fluidigm_pollen"}{Retrieved with

-#' \code{\link[scRNAseq]{ReprocessedFluidigmData}}. Returns a dataset of 65

+#' \code{\link{ReprocessedFluidigmData}}. Returns a dataset of 65

 #'  human neural cells from Pollen et al. (2014), each sequenced at high and low

 #'  coverage (SRA accession SRP041736).}

 #' \item{"allen_tasic"}{Retrieved with

-#' \code{\link[scRNAseq]{ReprocessedAllenData}}. Returns a dataset of 379 mouse

+#' \code{\link{ReprocessedAllenData}}. Returns a dataset of 379 mouse

 #' brain cells from Tasic et al. (2016).}

 #' \item{"pbmc3k"}{Retrieved with \code{\link[TENxPBMCData]{TENxPBMCData}}.

 #'  2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.}

@@ -31,7 +31,7 @@

 #' frames instead of file paths. The default is FALSE.

 #' @param class Character. The class of the expression matrix stored in the SCE

 #'  object. Can be one of "Matrix" (as returned by

-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by

+#'  \link{readMM} function), or "matrix" (as returned by

 #'  \link[base]{matrix} function). Default "Matrix".

 #' @param annotFileHeader Whether there's a header (colnames) in the cell annotation file. Default is FALSE  

 #' @param annotFileRowName Which column is used as the rownames for the cell annotation file. Default is 1 (first column). 

@@ -41,7 +41,7 @@

 #' @param featureSep Separater used for the feature annotation file. Default is "\\t".

 #' @param gzipped Whether the input file is gzipped. Default is "auto" and it will automatically detect whether the file is gzipped. Other options is TRUE or FALSE. 

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link{DelayedArray} object or not. Default \code{TRUE}.

 #' @return a SingleCellExperiment object

 #' @export

@@ -4,7 +4,7 @@

 #' \linkS4class{SingleCellExperiment} object. These gene sets can be used in

 #' downstream quality control and analysis functions in \link{singleCellTK}.

 #' @param inSCE Input \linkS4class{SingleCellExperiment} object.

-#' @param file Character. Path to GMT file. See \link[GSEABase]{getGmt} for

+#' @param file Character. Path to GMT file. See \link{getGmt} for

 #' more information on reading GMT files.

 #' @param collectionName Character. Name of collection to add gene sets to.

 #' If this collection already exists in \code{inSCE}, then these gene sets will

@@ -37,7 +37,7 @@

 #' \link{importGeneSetsFromMSigDB} for importing MSigDB gene sets.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object

 #'  with gene set from \code{collectionName} output stored to the

-#'  \link[S4Vectors]{metadata} slot.

+#'  \link{metadata} slot.

 #' @examples

 #' data(scExample)

 #'

@@ -92,7 +92,7 @@ importGeneSetsFromGMT <- function(inSCE, file,

 #' Default \code{"rownames"}.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object

 #' with gene set from \code{collectionName} output stored to the

-#' \link[S4Vectors]{metadata} slot.

+#' \link{metadata} slot.

 #' @details The gene identifiers in gene sets in \code{geneSetList} will be

 #' mapped to the rownames of \code{inSCE} using the \code{by} parameter and

 #' stored in a \linkS4class{GeneSetCollection} object from package

@@ -169,7 +169,7 @@ importGeneSetsFromList <- function(inSCE, geneSetList,

 #' downstream quality control and analysis functions in \link{singleCellTK}.

 #' @param inSCE Input \linkS4class{SingleCellExperiment} object.

 #' @param geneSetCollection A \linkS4class{GeneSetCollection} object. See

-#' \link[GSEABase]{GeneSetCollection} for more details.

+#' \link{GeneSetCollection} for more details.

 #' @param collectionName Character. Name of collection to add gene sets to.

 #' If this collection already exists in \code{inSCE}, then these gene sets will

 #' be added to that collection. Any gene sets within the collection with the

@@ -190,7 +190,7 @@ importGeneSetsFromList <- function(inSCE, geneSetList,

 #' Default \code{"rownames"}.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object

 #' with gene set from \code{collectionName} output stored to the

-#' \link[S4Vectors]{metadata} slot.

+#' \link{metadata} slot.

 #' @details The gene identifiers in gene sets in the

 #' \code{GeneSetCollection} will be mapped to the rownames of

 #' \code{inSCE} using the \code{by} parameter and

@@ -315,7 +315,7 @@ importGeneSetsFromCollection <- function(inSCE, geneSetCollection,

 #' @param verbose Boolean. Whether to display progress. Default \code{TRUE}.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object

 #' with gene set from \code{collectionName} output stored to the

-#' \link[S4Vectors]{metadata} slot.

+#' \link{metadata} slot.

 #' @details The gene identifiers in gene sets from MSigDB will be retrieved

 #' using the \code{\link{msigdbr}} package. They will be mapped to the IDs in

 #' \code{inSCE} using the \code{by} parameter and

@@ -2,7 +2,7 @@

 #' Imports samples from different sources and compiles them into a list of SCE objects

 #' @param allImportEntries object containing the sources and parameters of all the samples being imported (from the UI)

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link{DelayedArray} object or not. Default \code{TRUE}.

 #' @return A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing

 #' the droplet or cell data or both,depending on the dataType that users provided.

 #' @export

@@ -243,10 +243,10 @@

 #'  optimus_v1.4.0.

 #' @param class Character. The class of the expression matrix stored in the SCE

 #'  object. Can be one of "Matrix" (as returned by

-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by

+#'  \link{readMM} function), or "matrix" (as returned by

 #'  \link[base]{matrix} function). Default "Matrix".

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link{DelayedArray} object or not. Default \code{TRUE}.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object

 #'  containing the count

 #'  matrix, the gene annotation, and the cell annotation.

@@ -107,10 +107,10 @@

 #'  length as \code{samples}.

 #' @param class Character. The class of the expression matrix stored in the SCE

 #'  object. Can be one of "Matrix" (as returned by

-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by

+#'  \link{readMM} function), or "matrix" (as returned by

 #'  \link[base]{matrix} function). Default "Matrix".

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link{DelayedArray} object or not. Default \code{TRUE}.

 #' @return A \code{SingleCellExperiment} object containing the count

 #'  matrix, the gene annotation, and the cell annotation.

 #' @examples

@@ -164,10 +164,10 @@

 #' Default \code{FALSE}.

 #' @param class Character. The class of the expression matrix stored in the SCE

 #'  object. Can be one of "Matrix" (as returned by

-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by

+#'  \link{readMM} function), or "matrix" (as returned by

 #'  \link[base]{matrix} function). Default "Matrix".

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link{DelayedArray} object or not. Default \code{TRUE}.

 #' @param feNotFirstCol Boolean. \code{TRUE} if first column of

 #'  sparse_counts_genes.csv

 #' is row index and it will be removed. \code{FALSE} the first column will

@@ -40,7 +40,7 @@

 #' @param axis Choose from \code{"col"} or \code{"row"}.

 #' @param colorGen A function that generates color code vector by giving an

 #' integer for the number of colors. Alternatively,

-#' \code{\link[grDevices]{rainbow}}. Default \code{\link{distinctColors}}.

+#' \code{\link{rainbow}}. Default \code{\link{distinctColors}}.

 #' @return A \code{list} object containing distinct colors mapped to all

 #' possible categorical entries in \code{rowData(inSCE)} or

 #' \code{colData(inSCE)}.

@@ -36,14 +36,14 @@

 #'  will convert to a sparse format which should be used

 #'  for datasets with large numbers of cells.  Default "Matrix".

 #' @param delayedArray Boolean. Whether to read the expression matrix as

-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.

+#'  \link{DelayedArray} object or not. Default \code{TRUE}.

 #' @param colIndexLocation Character. For Optimus output, the path to the

 #'  barcode index .npy file. Used only if \code{file} has .npz extension.

 #'  Default \code{NULL}.

 #' @param rowIndexLocation Character. For Optimus output, The path to the

 #'  feature (gene) index .npy file. Used only if \code{file} has .npz extension.

 #'  Default \code{NULL}.

-#' @return A \link[DelayedArray]{DelayedArray} object or matrix.

+#' @return A \link{DelayedArray} object or matrix.

 #' @examples

 #' mat <- readSingleCellMatrix(system.file("extdata/hgmm_1k_v3_20x20/outs/",

 #'     "filtered_feature_bc_matrix/matrix.mtx.gz", package = "singleCellTK"))

@@ -30,7 +30,7 @@ ad <- NULL

 #' @name sctkPythonInstallConda

 #' @title Installs Python packages into a Conda environment

 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package

-#' using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This

+#' using \code{\link{conda_install}} from package \code{\link{reticulate}}. This

 #' will create a new Conda environment with the name \code{envname} if not already present.

 #' Note that Anaconda or Miniconda already need to be installed on the local system.

 #' @param envname Character. Name of the conda environment to create.

@@ -42,15 +42,15 @@ ad <- NULL

 #' @param pipIgnoreInstalled Boolean. Ignore installed versions when using pip. This is TRUE by default so that specific package versions can be installed even if they are downgrades.

 #'        The FALSE option is useful for situations where you don't want a pip install to attempt an overwrite of a conda binary package (e.g. SciPy on Windows which is very difficult

 #'        to install via pip due to compilation requirements).

-#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.

-#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}.

+#' @param pythonVersion Passed to \code{python_version} variable in \code{\link{conda_install}}. Default NULL.

+#' @param ... Other parameters to pass to \code{\link{conda_install}}.

 #' @return None. Installation of Conda environment.

 #' @examples

 #' \dontrun{

 #' sctkPythonInstallConda(envname = "sctk-reticulate")

 #' }

-#' @seealso See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment.

-#' See \code{\link[reticulate]{conda_install}} for more description of the installation parameters.

+#' @seealso See \code{\link{conda_create}} for more information on creating a Conda environment.

+#' See \code{\link{conda_install}} for more description of the installation parameters.

 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

 #' See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without

 #' going through the whole installation process again.

@@ -88,7 +88,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' @name sctkPythonInstallVirtualEnv

 #' @title Installs Python packages into a virtual environment

 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package

-#' using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This

+#' using \code{\link{virtualenv_install}} from package \code{\link{reticulate}}. This

 #' will create a new virtual environment with the name \code{envname} if not already present.

 #' @param envname Character. Name of the virtual environment to create.

 #' @param packages Character Vector. List of packages to install.

@@ -99,8 +99,8 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' \dontrun{

 #' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")

 #' }

-#' @seealso See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment.

-#' See \code{\link[reticulate]{virtualenv_install}} for more description of the installation parameters.

+#' @seealso See \code{\link{virtualenv_create}} for more information on creating a Conda environment.

+#' See \code{\link{virtualenv_install}} for more description of the installation parameters.

 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.

 #' See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without

 #' going through the whole installation process again.

@@ -7,7 +7,7 @@

 #' @param useAssay A single character indicating the name of the assay requiring

 #' batch correction. Default \code{"logcounts"}.

 #' @param batch A single character indicating a field in

-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.

+#' \code{\link{colData}} that annotates the batches.

 #' Default \code{"batch"}.

 #' @param reducedDimName A single character. The name for the corrected

 #' low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.

@@ -71,7 +71,7 @@ runBBKNN <-function(inSCE, useAssay = 'logcounts', batch = 'batch',

 #' @param useAssay A single character indicating the name of the assay requiring

 #' batch correction. Default \code{"logcounts"}.

 #' @param batch A single character indicating a field in

-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.

+#' \code{\link{colData}} that annotates the batches.

 #' Default \code{"batch"}.

 #' @param par.prior A logical scalar. TRUE indicates parametric adjustments

 #' will be used, FALSE indicates non-parametric adjustments will be used.

@@ -83,7 +83,7 @@ runBBKNN <-function(inSCE, useAssay = 'logcounts', batch = 'batch',

 #' @param ref.batch If given, will use the selected batch as a reference for

 #' batch adjustment. Default \code{NULL}.

 #' @param assayName A single characeter. The name for the corrected assay. Will

-#' be saved to \code{\link[SummarizedExperiment]{assay}}. Default

+#' be saved to \code{\link{assay}}. Default

 #' \code{"ComBat"}.

 #' @return The input \linkS4class{SingleCellExperiment} object with

 #' \code{assay(inSCE, assayName)} updated.

@@ -143,7 +143,7 @@ runComBat <- function(inSCE, useAssay = "logcounts", batch = 'batch',

 #' batch correction. Default \code{"logcounts"}. Alternatively, see

 #' \code{pcInput} parameter.

 #' @param batch A single character indicating a field in

-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.

+#' \code{\link{colData}} that annotates the batches.

 #' Default \code{"batch"}.

 #' @param reducedDimName A single character. The name for the corrected

 #' low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.

@@ -208,7 +208,7 @@ runFastMNN <- function(inSCE, useAssay = "logcounts",

 # #' @param useAssay A single character indicating the name of the assay requiring

 # #' batch correction. Default \code{"logcounts"}.

 # #' @param batch A single character indicating a field in

-# #' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.

+# #' \code{\link{colData}} that annotates the batches.

 # #' Default \code{"batch"}.

 # #' @param reducedDimName A single character. The name for the corrected

 # #' low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.

@@ -282,7 +282,7 @@ runFastMNN <- function(inSCE, useAssay = "logcounts",

 # #' @param useAssay A single character indicating the name of the assay requiring

 # #' batch correction. Default \code{"logcounts"}.

 # #' @param batch A single character indicating a field in

-# #' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.

+# #' \code{\link{colData}} that annotates the batches.

 # #' Default \code{"batch"}.

 # #' @param reducedDimName A single character. The name for the corrected

 # #' low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.

@@ -360,10 +360,10 @@ runFastMNN <- function(inSCE, useAssay = "logcounts",

 #' @param useAssay A single character indicating the name of the assay requiring

 #' batch correction. Default \code{"logcounts"}.

 #' @param batch A single character indicating a field in

-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.

+#' \code{\link{colData}} that annotates the batches.

 #' Default \code{"batch"}.

 #' @param assayName A single characeter. The name for the corrected assay. Will

-#' be saved to \code{\link[SummarizedExperiment]{assay}}. Default

+#' be saved to \code{\link{assay}}. Default

 #' \code{"LIMMA"}.

 #' @return The input \linkS4class{SingleCellExperiment} object with

 #' \code{assay(inSCE, assayName)} updated.

@@ -408,7 +408,7 @@ runLimmaBC <- function(inSCE, useAssay = "logcounts", assayName = "LIMMA",

 #' @param useAssay A single character indicating the name of the assay requiring

 #' batch correction. Default \code{"logcounts"}.

 #' @param batch A single character indicating a field in

-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.

+#' \code{\link{colData}} that annotates the batches.

 #' Default \code{"batch"}.

 #' @param k An integer. Specifies the number of nearest neighbours to

 #' consider when defining MNN pairs. This should be interpreted as the minimum

@@ -423,7 +423,7 @@ runLimmaBC <- function(inSCE, useAssay = "logcounts", assayName = "LIMMA",

 #' which may be more accurate but comes at the cost of precision. Default

 #' \code{0.1}.

 #' @param assayName A single characeter. The name for the corrected assay. Will

-#' be saved to \code{\link[SummarizedExperiment]{assay}}. Default

+#' be saved to \code{\link{assay}}. Default

 #' \code{"MNN"}.

 #' @return The input \linkS4class{SingleCellExperiment} object with

 #' \code{assay(inSCE, assayName)} updated.

@@ -467,7 +467,7 @@ runMNNCorrect <- function(inSCE, useAssay = 'logcounts', batch = 'batch',

 #' @param useAssay A single character indicating the name of the assay requiring

 #' batch correction. Default \code{"logcounts"}.

 #' @param batch A single character indicating a field in

-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.

+#' \code{\link{colData}} that annotates the batches.

 #' Default \code{"batch"}.

 #' @param SIGMA A numeric scalar. Algorithmic parameter, correction smoothing

 #' parameter on Gaussian kernel. Default \code{15}.

@@ -476,7 +476,7 @@ runMNNCorrect <- function(inSCE, useAssay = 'logcounts', batch = 'batch',

 #' @param KNN An integer. Algorithmic parameter, number of nearest neighbors to

 #' use for matching. Default \code{20L}.

 #' @param assayName A single characeter. The name for the corrected assay. Will

-#' be saved to \code{\link[SummarizedExperiment]{assay}}. Default

+#' be saved to \code{\link{assay}}. Default

 #' \code{"SCANORAMA"}.

 #' @return The input \linkS4class{SingleCellExperiment} object with

 #' \code{assay(inSCE, assayName)} updated.

@@ -558,7 +558,7 @@ integrated = integrated[:, orderIdx]

 #' @param useAssay A single character indicating the name of the assay requiring

 #' batch correction. Default \code{"logcounts"}.

 #' @param batch A single character indicating a field in

-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.

+#' \code{\link{colData}} that annotates the batches.

 #' Default \code{"batch"}.

 #' @param kmeansK An integer vector. Indicating the kmeans' K-value for each

 #' batch (i.e. how many subclusters in each batch should exist), in order to

@@ -576,7 +576,7 @@ integrated = integrated[:, orderIdx]

 #' @param nCores An integer. The number of cores of processors to allocate for

 #' the task. Default \code{1L}.

 #' @param assayName A single characeter. The name for the corrected assay. Will

-#' be saved to \code{\link[SummarizedExperiment]{assay}}. Default

+#' be saved to \code{\link{assay}}. Default

 #' \code{"scMerge"}.

 #' @return The input \linkS4class{SingleCellExperiment} object with

 #' \code{assay(inSCE, assayName)} updated.

@@ -672,7 +672,7 @@ runSCMerge <- function(inSCE, useAssay = "logcounts", batch = 'batch',

 #' batch correction. Note that ZINBWaVE works for counts (integer) input rather

 #' than logcounts that other methods prefer. Default \code{"counts"}.

 #' @param batch A single character indicating a field in

-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.

+#' \code{\link{colData}} that annotates the batches.

 #' Default \code{"batch"}.

 #' @param nHVG An integer. Number of highly variable genes to use when fitting

 #' the model. Default \code{1000L}.

@@ -16,7 +16,7 @@

 #' @param seed Seed for the random number generator. Default 12345.

 #' @param paramsList A list containing parameters for QC functions. Default NULL.

 #' @return SingleCellExperiment object containing the outputs of the

-#'  specified algorithms in the \link[SummarizedExperiment]{colData}

+#'  specified algorithms in the \link{colData}

 #' of \code{inSCE}.

 #' @examples

 #' data(scExample, package = "singleCellTK")

@@ -137,7 +137,7 @@ runCellQC <- function(inSCE,

 #'  matrix for droplets.

 #' @param paramsList A list containing parameters for QC functions. Default NULL.

 #' @return SingleCellExperiment object containing the outputs of the

-#'  specified algorithms in the \link[SummarizedExperiment]{colData}

+#'  specified algorithms in the \link{colData}

 #' of \code{inSCE}.

 #' @examples

 #' data(scExample, package = "singleCellTK")

@@ -110,8 +110,7 @@

 #' @description  Creates a table of QC metrics generated from

 #'  QC algorithms via either kable or csv file.

 #' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved

-#' \link[SummarizedExperiment]{assay} data and/or

-#' \link[SummarizedExperiment]{colData} data. Required.

+#' \link{assay} data and/or \link{colData} data. Required.

 #' @param sample Character vector. Indicates which sample each cell belongs to.

 #' @param useAssay  A string specifying which assay in the SCE to use. Default

 #'  'counts'.

@@ -9,7 +9,7 @@

 #' If another character is supplied, then genes will be looked up in the column names of \code{rowData(inSCE)}. A character vector with the same length as \code{geneSetList} can be supplied if the IDs for different

 #' gene sets are found in different places, including a mixture of 'rownames' and \code{rowData(inSCE)}. An integer or integer vector can be supplied to denote the column index in \code{rowData(inSCE)}. Default 'rownames'.

 #' @param geneSetCollection Class of \code{GeneSetCollection} from package \code{GSEAbase}. The location of the gene IDs in \code{inSCE} should be in the \code{description} slot of each gene set and should follow the

-#' same notation as \code{geneSetListLocation}. The function \link[GSEABase]{getGmt} can be used to read in gene sets from a GMT file. If reading a GMT file, the second column for each gene set should be the description denoting the location

+#' same notation as \code{geneSetListLocation}. The function \link{getGmt} can be used to read in gene sets from a GMT file. If reading a GMT file, the second column for each gene set should be the description denoting the location

 #' of the gene IDs in \code{inSCE}. These gene sets will be included with those from \code{geneSetList} if both parameters are provided.

 #' @param percent_top An integer vector. Each element is treated as a

 #' number of top genes to compute the percentage of library size occupied by

@@ -23,10 +23,10 @@

 #' @param flatten Logical scalar indicating whether the nested \link[S4Vectors]{DataFrame-class}

 #' in the output should be flattened.

 #' @param detectionLimit A numeric scalar specifying the lower detection limit for expression.

-#' @param BPPARAM A \link[BiocParallel]{BiocParallelParam} object specifying

+#' @param BPPARAM A \link{BiocParallelParam} object specifying

 #' whether the QC calculations should be parallelized.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with

-#'  cell QC metrics added to the \link[SummarizedExperiment]{colData} slot. If \code{geneSetList} or \code{geneSetCollection} are provided, then the rownames for each gene set will be saved in \code{metadata(inSCE)$scater$addPerCellQC$geneSets}.

+#'  cell QC metrics added to the \link{colData} slot. If \code{geneSetList} or \code{geneSetCollection} are provided, then the rownames for each gene set will be saved in \code{metadata(inSCE)$scater$addPerCellQC$geneSets}.

 #' @examples

 #' data(scExample, package = "singleCellTK")

 #' mito.ix = grep("^MT-", rowData(sce)$feature_name)

@@ -1,5 +1,5 @@

 #' scater_logNormCounts

-#' Uses \link[scater]{logNormCounts} to log normalize input data

+#' Uses \link{logNormCounts} to log normalize input data

 #' @param inSCE Input SingleCellExperiment object

 #' @param logAssayName New assay name for log normalized data

 #' @param useAssay Input assay 

@@ -18,7 +18,7 @@

 #' @param useAssay  A string specifying which assay in the SCE to use.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with

 #'  \link[scds]{cxds} output appended to the

-#'  \link[SummarizedExperiment]{colData} slot. The columns include

+#'  \link{colData} slot. The columns include

 #'  \emph{cxds_score} and optionally \emph{cxds_call}.

 #'  Please refer to the documentation of \link[scds]{cxds} for details.

 #' @examples

@@ -130,7 +130,7 @@ runCxds <- function(inSCE,

 #' @param useAssay  A string specifying which assay in the SCE to use.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with

 #'  \link[scds]{bcds} output appended to the

-#'  \link[SummarizedExperiment]{colData} slot. The columns include

+#'  \link{colData} slot. The columns include

 #'  \emph{bcds_score} and optionally \emph{bcds_call}.

 #'  Please refer to the documentation of \link[scds]{bcds} for details.

 #' @examples

@@ -250,7 +250,7 @@ runBcds <- function(inSCE,

 #' @param useAssay  A string specifying which assay in the SCE to use.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with

 #'  \link[scds]{cxds_bcds_hybrid} output appended to the

-#'  \link[SummarizedExperiment]{colData} slot. The columns include

+#'  \link{colData} slot. The columns include

 #'  \emph{hybrid_score} and optionally \emph{hybrid_call}.

 #'  Please refer to the documentation of \link[scds]{cxds_bcds_hybrid} for

 #'  details.

@@ -72,16 +72,16 @@

 #' This should be an algorithm supported by \code{\link[BiocNeighbors]{findNeighbors}}.

 #' @param BSPARAM A \code{\link[BiocSingular]{BiocSingularParam}} object specifying the algorithm to

 #'  use for PCA, if \code{d} is not \code{NA}.

-#' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} object specifying whether the

+#' @param BPPARAM A \code{\link{BiocParallelParam}} object specifying whether the

 #'  neighbour searches should be parallelized.

 #' @details This function is a wrapper function for \link[scran]{doubletCells}.

 #'  \code{runDoubletCells} runs \link[scran]{doubletCells} for each

 #'  \code{sample} within \code{inSCE} iteratively. The

 #'  resulting doublet scores for all cells will be appended to the

-#'  \link[SummarizedExperiment]{colData} of \code{inSCE}.

+#'  \link{colData} of \code{inSCE}.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with the

 #'  'scran_doubletCells_score' column added to the

-#'  \link[SummarizedExperiment]{colData} slot.

+#'  \link{colData} slot.

 #' @references Lun ATL (2018). Detecting doublet cells with scran.

 #'  \url{https://ltla.github.io/SingleCellThoughts/software/

 #' doublet_detection/bycell.html}

@@ -75,7 +75,7 @@

 #' @param seed Seed for the random number generator. Default 12345.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with

 #'  \code{scrub_doublets} output appended to the

-#'  \link[SummarizedExperiment]{colData} slot. The columns include

+#'  \link{colData} slot. The columns include

 #'  \emph{scrublet_score} and \emph{scrublet_call}.

 #' @examples

 #' data(scExample, package = "singleCellTK")

@@ -494,7 +494,7 @@ seuratHeatmapPlot <- function(plotObject, dims, ncol, labels) {

 #' @param seuratDataSlot Selected data slot from the Seurat object. Default \code{"counts"}.

 #' @param seuratAssaySlot Selected assay from Seurat object. Default \code{"RNA"}.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with

-#'  data from Seurat object appended to the \link[SummarizedExperiment]{assay} slot.

+#'  data from Seurat object appended to the \link{assay} slot.

 #' @importFrom SummarizedExperiment assay<-

 .updateAssaySCE <- function(inSCE, seuratObject, assaySlotSCE, seuratDataSlot = "counts", seuratAssaySlot = "RNA") {

   assay(inSCE, assaySlotSCE) <- NULL

@@ -6,7 +6,7 @@

 #' with one another. If \code{returnAsAltExp} is set to \code{TRUE},

 #' then the returned object will have the same number of rows as the input

 #' \code{inSCE} as the subsetted object will be stored in the

-#' \code{\link[SingleCellExperiment]{altExp}} slot.

+#' \code{\link{altExp}} slot.

 #' @param inSCE Input \linkS4class{SingleCellExperiment} object.

 #' @param index Integer vector. Vector of indicies indicating which rows

 #' to keep. If \code{NULL}, this will not be used for subsetting.

@@ -15,7 +15,7 @@ dataAnnotationColor(inSCE, axis = NULL, colorGen = distinctColors)

 \item{colorGen}{A function that generates color code vector by giving an

 integer for the number of colors. Alternatively,

-\code{\link[grDevices]{rainbow}}. Default \code{\link{distinctColors}}.}

+\code{\link{rainbow}}. Default \code{\link{distinctColors}}.}

 }

 \value{

 A \code{list} object containing distinct colors mapped to all

@@ -26,7 +26,7 @@ Update/Modify/Add an assay in the provided SingleCellExperiment object from a Se

 }

 \value{

 A \link[SingleCellExperiment]{SingleCellExperiment} object with

- data from Seurat object appended to the \link[SummarizedExperiment]{assay} slot.

+ data from Seurat object appended to the \link{assay} slot.

 }

 \description{

 .updateAssaySCE

@@ -33,13 +33,13 @@ selected.variable features. Default \code{NULL}.}

 \item{sample}{Character vector. Indicates which sample each cell belongs to.

 If given a single character, will take the annotation from

-\code{\link[SummarizedExperiment]{colData}}. Default \code{NULL}.}

+\code{\link{colData}}. Default \code{NULL}.}

 \item{reducedDimName}{A name to store the results of the dimension reduction

 coordinates obtained from this method. Default \code{"UMAP"}.}

 \item{logNorm}{Whether the counts will need to be log-normalized prior to

-generating the UMAP via \code{\link[scater]{logNormCounts}}. Default

+generating the UMAP via \code{\link{logNormCounts}}. Default

 \code{TRUE}.}

 \item{nNeighbors}{The size of local neighborhood used for manifold

@@ -60,7 +60,7 @@ result on a more even dispersal of points. Default \code{0.01}. See

 `?uwot::umap` for more information.}

 \item{spread}{The effective scale of embedded points. In combination with

-‘min_dist’, this determines how clustered/clumped the embedded points are.

+minDist, this determines how clustered/clumped the embedded points are.

 Default \code{1}. See `?uwot::umap` for more information.}

 \item{pca}{Logical. Whether to perform dimension reduction with PCA before

@@ -30,7 +30,7 @@ Can be one of -

 }}

 \item{delayedArray}{Boolean. Whether to read the expression matrix as

-\link[DelayedArray]{DelayedArray} object. Default \code{TRUE}.}

+\link{DelayedArray} object. Default \code{TRUE}.}

 }

 \value{

 A \code{SingleCellExperiment} object.

@@ -42,11 +42,11 @@ files are gzip compressed. Must have length 1 or the same length as

 \item{class}{Character. The class of the expression matrix stored in the SCE

 object. Can be one of "Matrix" (as returned by

-\link[Matrix]{readMM} function), or "matrix" (as returned by

+\link{readMM} function), or "matrix" (as returned by

 \link[base]{matrix} function). Default "Matrix".}

 \item{delayedArray}{Boolean. Whether to read the expression matrix as

-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}

+\link[DelayedArray]{DelayedArray-class} object or not. Default \code{TRUE}.}

 }

 \value{

 A \code{SingleCellExperiment} object containing the count

@@ -50,7 +50,7 @@ argument.}

 \itemize{

   \item \code{NULL}. All samples within \code{cellRangerDirs} will be

    imported. The order of samples will be first determined by the order of

-   \code{cellRangerDirs} and then by \link[base]{list.dirs}. This is only

+   \code{cellRangerDirs} and then by \link{list.dirs}. This is only

    for the case where \code{cellRangerDirs} is specified.

   \item A list of vectors containing the folder names for samples to import.

    Each vector in

@@ -134,11 +134,11 @@ order match the output of

 \item{class}{Character. The class of the expression matrix stored in the SCE

 object. Can be one of "Matrix" (as returned by

-\link[Matrix]{readMM} function), or "matrix" (as returned by

+\link{readMM} function), or "matrix" (as returned by

 \link[base]{matrix} function). Default \code{"Matrix"}.}

 \item{delayedArray}{Boolean. Whether to read the expression matrix as

-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}

+\link{DelayedArray} object or not. Default \code{TRUE}.}

 \item{dataTypeV2}{Character. The type of output to import for

 Cellranger version below 3.0.0. Whether to import the filtered or the 

@@ -19,11 +19,11 @@ Default "sample".}

 \item{class}{Character. The class of the expression matrix stored in the SCE

 object. Can be one of "Matrix" (as returned by

-\link[Matrix]{readMM} function), or "matrix" (as returned by

+\link{readMM} function), or "matrix" (as returned by

 \link[base]{matrix} function). Default "Matrix".}

 \item{delayedArray}{Boolean. Whether to read the expression matrix as

-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}

+\link{DelayedArray} object or not. Default \code{TRUE}.}

 }

 \value{

 A \code{SingleCellExperiment} object containing the count

@@ -19,11 +19,11 @@ Default "sample".}

 \item{class}{Character. The class of the expression matrix stored in the SCE

 object. Can be one of "Matrix" (as returned by

-\link[Matrix]{readMM} function), or "matrix" (as returned by

+\link{readMM} function), or "matrix" (as returned by

 \link[base]{matrix} function). Default "Matrix".}

 \item{delayedArray}{Boolean. Whether to read the expression matrix as

-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}

+\link{DelayedArray} object or not. Default \code{TRUE}.}

 }

 \value{

 A \code{SingleCellExperiment} object containing the count

@@ -23,7 +23,7 @@ importDropEst(

 Default "sample".}

 \item{delayedArray}{Boolean. Whether to read the expression matrix as

-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}

+\link{DelayedArray} object or not. Default \code{TRUE}.}

 }

 \value{

 A \code{SingleCellExperiment} object containing the count matrix,

@@ -16,7 +16,7 @@ will store the data as a sparse matrix from package \link{Matrix} while

 \code{"Matrix"}.}

 \item{delayedArray}{Boolean. Whether to read the expression matrix as

-\link[DelayedArray]{DelayedArray} object or not. Default \code{FALSE}.}

+\link{DelayedArray} object or not. Default \code{FALSE}.}

 }

 \value{

 The specified \link[SingleCellExperiment]{SingleCellExperiment} object.

@@ -24,7 +24,7 @@ The specified \link[SingleCellExperiment]{SingleCellExperiment} object.

 \description{

 Retrieves published example datasets stored in

 \link[SingleCellExperiment]{SingleCellExperiment} using the

-\link[scRNAseq]{scRNAseq} and

+\link{scRNAseq} and

 \link[TENxPBMCData]{TENxPBMCData} packages. See 'Details' for a

 list of available datasets.

 }

@@ -33,11 +33,11 @@ See the list below for the available datasets and their

 descriptions.

 \describe{

 \item{"fluidigm_pollen"}{Retrieved with

-\code{\link[scRNAseq]{ReprocessedFluidigmData}}. Returns a dataset of 65

+\code{\link{ReprocessedFluidigmData}}. Returns a dataset of 65

  human neural cells from Pollen et al. (2014), each sequenced at high and low

  coverage (SRA accession SRP041736).}

 \item{"allen_tasic"}{Retrieved with

-\code{\link[scRNAseq]{ReprocessedAllenData}}. Returns a dataset of 379 mouse

+\code{\link{ReprocessedAllenData}}. Returns a dataset of 379 mouse

 brain cells from Tasic et al. (2016).}

 \item{"pbmc3k"}{Retrieved with \code{\link[TENxPBMCData]{TENxPBMCData}}.

  2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.}

@@ -42,11 +42,11 @@ frames instead of file paths. The default is FALSE.}

 \item{class}{Character. The class of the expression matrix stored in the SCE

 object. Can be one of "Matrix" (as returned by

-\link[Matrix]{readMM} function), or "matrix" (as returned by

+\link{readMM} function), or "matrix" (as returned by

 \link[base]{matrix} function). Default "Matrix".}

 \item{delayedArray}{Boolean. Whether to read the expression matrix as

-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}

+\link{DelayedArray} object or not. Default \code{TRUE}.}

 \item{annotFileHeader}{Whether there's a header (colnames) in the cell annotation file. Default is FALSE}

@@ -15,7 +15,7 @@ importGeneSetsFromCollection(

 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object.}

 \item{geneSetCollection}{A \linkS4class{GeneSetCollection} object. See

-\link[GSEABase]{GeneSetCollection} for more details.}

+\link{GeneSetCollection} for more details.}

 \item{collectionName}{Character. Name of collection to add gene sets to.

 If this collection already exists in \code{inSCE}, then these gene sets will