diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
index ce93b914d..e58097185 100644
--- a/.github/workflows/rworkflows.yml
+++ b/.github/workflows/rworkflows.yml
@@ -14,8 +14,7 @@ name: rworkflows
     - RELEASE_**
 jobs:
   rworkflows:
-    permissions:
-      contents: write
+    permissions: write-all
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}
@@ -26,8 +25,8 @@ jobs:
         - os: ubuntu-latest
           bioc: devel
           r: auto
-          cont: bioconductor/bioconductor_docker:devel
-          rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release
+          cont: ghcr.io/bioconductor/bioconductor_docker:devel
+          rspm: ~
         - os: macOS-latest
           bioc: devel
           r: auto
@@ -55,4 +54,4 @@ jobs:
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}
         cache_version: cache-v1
-        enable_act: ${{ false }}
+        docker_registry: ghcr.io
\ No newline at end of file
diff --git a/R/agglomerate.R b/R/agglomerate.R
index d03a30f35..e364bfadb 100644
--- a/R/agglomerate.R
+++ b/R/agglomerate.R
@@ -49,20 +49,20 @@
 #'   to \code{getPrevalence} and \code{getPrevalentTaxa} and used in 
 #'   \code{agglomeratebyPrevalence}
 #'   \itemize{
-#'        \item{\code{remove_empty_ranks}}{A single boolean value for selecting 
+#'        \item \code{remove_empty_ranks}: A single boolean value for selecting 
 #'        whether to remove those columns of rowData that include only NAs after
-#'        agglomeration. (By default: \code{remove_empty_ranks = FALSE})}
-#'        \item{\code{make_unique}}{A single boolean value for selecting 
-#'        whether to make rownames unique. (By default: \code{make_unique = TRUE})}
-#'        \item{\code{detection}}{Detection threshold for absence/presence. 
+#'        agglomeration. (By default: \code{remove_empty_ranks = FALSE})
+#'        \item \code{make_unique}: A single boolean value for selecting 
+#'        whether to make rownames unique. (By default: \code{make_unique = TRUE})
+#'        \item \code{detection}: Detection threshold for absence/presence. 
 #'        Either an absolute value compared directly to the values of \code{x} 
-#'        or a relative value between 0 and 1, if \code{as_relative = FALSE}.}
-#'        \item{\code{prevalence}}{Prevalence threshold (in 0 to 1). The 
+#'        or a relative value between 0 and 1, if \code{as_relative = FALSE}.
+#'        \item \code{prevalence}: Prevalence threshold (in 0 to 1). The 
 #'        required prevalence is strictly greater by default. To include the 
-#'        limit, set \code{include_lowest} to \code{TRUE}.}
-#'        \item{\code{as.relative}}{Logical scalar: Should the detection 
+#'        limit, set \code{include_lowest} to \code{TRUE}.
+#'        \item \code{as.relative}: Logical scalar: Should the detection 
 #'        threshold be applied on compositional (relative) abundances? 
-#'        (default: \code{FALSE})}
+#'        (default: \code{FALSE})
 #'    }
 #'
 #' @param altexp String or integer scalar specifying an alternative experiment
diff --git a/R/decontam.R b/R/decontam.R
index c55523231..4b277999a 100644
--- a/R/decontam.R
+++ b/R/decontam.R
@@ -47,11 +47,11 @@
 #'
 #' @param ... 
 #' \itemize{
-#'   \item{for \code{isContaminant}/ \code{isNotContaminant}: }{arguments
+#'   \item for \code{isContaminant}/ \code{isNotContaminant}: arguments
 #'     passed on to \code{\link[decontam:isContaminant]{decontam:isContaminant}}
-#'     or \code{\link[decontam:isNotContaminant]{decontam:isNotContaminant}}}
-#'   \item{for \code{addContaminantQC}/\code{addNotContaminantQC}: }{arguments
-#'     passed on to \code{isContaminant}/ \code{isNotContaminant}}
+#'     or \code{\link[decontam:isNotContaminant]{decontam:isNotContaminant}}
+#'   \item for \code{addContaminantQC}/\code{addNotContaminantQC}: arguments
+#'     passed on to \code{isContaminant}/ \code{isNotContaminant}
 #' }
 #'
 #' @return for \code{isContaminant}/ \code{isNotContaminant} a \code{DataFrame}
diff --git a/R/estimateDiversity.R b/R/estimateDiversity.R
index be257b5e1..f8ca43e18 100644
--- a/R/estimateDiversity.R
+++ b/R/estimateDiversity.R
@@ -46,20 +46,20 @@
 #'
 #' @param ... optional arguments:
 #' \itemize{
-#'   \item{threshold}{ A numeric value in the unit interval,
+#'   \item threshold: A numeric value in the unit interval,
 #'   determining the threshold for coverage index. By default,
-#'   \code{threshold} is 0.9.}
-#'   \item{quantile}{ Arithmetic abundance classes are evenly cut up to to
+#'   \code{threshold} is 0.9.
+#'   \item quantile: Arithmetic abundance classes are evenly cut up to to
 #'   this quantile of the data. The assumption is that abundances higher than
 #'   this are not common, and they are classified in their own group.
-#'   By default, \code{quantile} is 0.5.}
-#'   \item{num_of_classes}{ The number of arithmetic abundance classes
+#'   By default, \code{quantile} is 0.5.
+#'   \item num_of_classes: The number of arithmetic abundance classes
 #'   from zero to the quantile cutoff indicated by \code{quantile}. 
-#'   By default, \code{num_of_classes} is 50.}
-#'   \item{only.tips}{ A boolean value specifying whether to remove internal
+#'   By default, \code{num_of_classes} is 50.
+#'   \item only.tips: A boolean value specifying whether to remove internal
 #'   nodes when Faith's index is calculated. When \code{only.tips=TRUE}, those
 #'   rows that are not tips of tree are removed.
-#'   (By default: \code{only.tips=FALSE})}
+#'   (By default: \code{only.tips=FALSE})
 #' }
 #'
 #' @return \code{x} with additional \code{\link{colData}} named \code{*name*}
@@ -74,11 +74,11 @@
 #'
 #' \itemize{
 #' 
-#' \item{'coverage' }{Number of species needed to cover a given fraction of
+#' \item 'coverage': Number of species needed to cover a given fraction of
 #' the ecosystem (50 percent by default). Tune this with the threshold
-#' argument.}
+#' argument.
 #' 
-#' \item{'faith' }{Faith's phylogenetic alpha diversity index measures how
+#' \item 'faith': Faith's phylogenetic alpha diversity index measures how
 #' long the taxonomic distance is between taxa that are present in the sample.
 #' Larger values represent higher diversity. Using this index requires
 #' rowTree. (Faith 1992)
@@ -87,12 +87,12 @@
 #' internal nodes, there are two options. First, you can keep those features,
 #' and prune the tree to match features so that each tip can be found from
 #' the features. Other option is to remove all features that are not tips.
-#' (See \code{only.tips} parameter)}
+#' (See \code{only.tips} parameter)
 #' 
-#' \item{'fisher' }{Fisher's alpha; as implemented in
-#' \code{\link[vegan:diversity]{vegan::fisher.alpha}}. (Fisher et al. 1943)}
+#' \item 'fisher': Fisher's alpha; as implemented in
+#' \code{\link[vegan:diversity]{vegan::fisher.alpha}}. (Fisher et al. 1943)
 #' 
-#' \item{'gini_simpson' }{Gini-Simpson diversity i.e. \eqn{1 - lambda},
+#' \item 'gini_simpson': Gini-Simpson diversity i.e. \eqn{1 - lambda},
 #' where \eqn{lambda} is the
 #' Simpson index, calculated as the sum of squared relative abundances.
 #' This corresponds to the diversity index
@@ -101,25 +101,25 @@
 #' psychology and management studies. The Gini-Simpson index (1-lambda)
 #' should not be
 #' confused with Simpson's dominance (lambda), Gini index, or
-#' inverse Simpson index (1/lambda).}
+#' inverse Simpson index (1/lambda).
 #' 
-#' \item{'inverse_simpson' }{Inverse Simpson diversity:
+#' \item 'inverse_simpson': Inverse Simpson diversity:
 #' \eqn{1/lambda} where \eqn{lambda=sum(p^2)} and p refers to relative
 #' abundances.
 #' This corresponds to the diversity index
 #' 'invsimpson' in vegan::diversity. Don't confuse this with the
-#' closely related Gini-Simpson index}
+#' closely related Gini-Simpson index
 #'
-#' \item{'log_modulo_skewness' }{The rarity index characterizes the
+#' \item 'log_modulo_skewness': The rarity index characterizes the
 #' concentration of species at low abundance. Here, we use the skewness of
 #' the frequency 
 #' distribution of arithmetic abundance classes (see Magurran & McGill 2011).
 #' These are typically right-skewed; to avoid taking log of occasional
 #' negative skews, we follow Locey & Lennon (2016) and use the log-modulo
 #' transformation that adds a value of one to each measure of skewness to
-#' allow logarithmization.}
+#' allow logarithmization.
 #'
-#' \item{'shannon' }{Shannon diversity (entropy).}
+#' \item 'shannon': Shannon diversity (entropy).
 #' 
 #' }
 #'
@@ -158,11 +158,11 @@
 #' @seealso
 #' \code{\link[scater:plotColData]{plotColData}}
 #' \itemize{
-#'   \item{\code{\link[mia:estimateRichness]{estimateRichness}}}
-#'   \item{\code{\link[mia:estimateEvenness]{estimateEvenness}}}
-#'   \item{\code{\link[mia:estimateDominance]{estimateDominance}}}
-#'   \item{\code{\link[vegan:diversity]{diversity}}}
-#'   \item{\code{\link[vegan:specpool]{estimateR}}}
+#'   \item \code{\link[mia:estimateRichness]{estimateRichness}}
+#'   \item \code{\link[mia:estimateEvenness]{estimateEvenness}}
+#'   \item \code{\link[mia:estimateDominance]{estimateDominance}}
+#'   \item \code{\link[vegan:diversity]{diversity}}
+#'   \item \code{\link[vegan:specpool]{estimateR}}
 #' }
 #'
 #' @name estimateDiversity
@@ -258,7 +258,7 @@ setMethod("estimateDiversity", signature = c(x="SummarizedExperiment"),
                              "inverse_simpson", "log_modulo_skewness", "shannon")
         index_string <- paste0("'", paste0(supported_index, collapse = "', '"), "'")
         if ( !all(index %in% supported_index) || !(length(index) > 0)) {
-            stop("'", paste0("'index' must be from the following options: '",supported_types), "'", call. = FALSE)
+            stop("'", paste0("'index' must be from the following options: '",index_string), "'", call. = FALSE)
         }
         
         if(!.is_non_empty_character(name) || length(name) != length(index)){
diff --git a/R/estimateDominance.R b/R/estimateDominance.R
index 733de5538..269bd2064 100644
--- a/R/estimateDominance.R
+++ b/R/estimateDominance.R
@@ -60,11 +60,11 @@
 #'
 #' \itemize{
 #' 
-#' \item{'absolute' }{Absolute index equals to the absolute abundance of the
+#' \item 'absolute': Absolute index equals to the absolute abundance of the
 #' most dominant n species of the sample (specify the number with the argument
-#' \code{ntaxa}). Index gives positive integer values.}
+#' \code{ntaxa}). Index gives positive integer values.
 #' 
-#' \item{'dbp' }{Berger-Parker index (See Berger & Parker 1970) calculation
+#' \item 'dbp': Berger-Parker index (See Berger & Parker 1970) calculation
 #' is a special case of the 'relative' index. dbp is the relative abundance of
 #' the most
 #' abundant species of the sample. Index gives values in interval 0 to 1,
@@ -73,9 +73,9 @@
 #' \deqn{dbp = \frac{N_1}{N_{tot}}}{%
 #' dbp = N_1/N_tot} where \eqn{N_1} is the absolute abundance of the most
 #' dominant species and \eqn{N_{tot}} is the sum of absolute abundances of all
-#' species.}
+#' species.
 #' 
-#' \item{'core_abundance' }{ Core abundance index is related to core species.
+#' \item 'core_abundance': Core abundance index is related to core species.
 #' Core species are species that are most abundant in all samples, i.e., in
 #' whole data set. Core species are defined as those species that have
 #' prevalence over 50\%. It means that in order to belong to core species,
@@ -87,9 +87,9 @@
 #' \deqn{core_abundance = \frac{N_{core}}{N_{tot}}}{%
 #' core_abundance = N_core/N_tot} where \eqn{N_{core}} is the sum of absolute
 #' abundance of the core species and \eqn{N_{tot}} is the sum of absolute
-#' abundances of all species.}
+#' abundances of all species.
 #' 
-#' \item{'gini' }{ Gini index is probably best-known from socio-economic
+#' \item 'gini':  Gini index is probably best-known from socio-economic
 #' contexts (Gini 1921). In economics, it is used to measure, for example, how
 #' unevenly income is distributed among population. Here, Gini index is used
 #' similarly, but income is replaced with abundance. 
@@ -98,9 +98,9 @@
 #' that represent large portion of total abundance of microbes, the inequality
 #' is large and Gini index closer to 1. If all species has equally large
 #' abundances, the equality is perfect and Gini index equals 0. This index
-#' should not be confused with Gini-Simpson index, which quantifies diversity.}
+#' should not be confused with Gini-Simpson index, which quantifies diversity.
 #'
-#' \item{'dmn' }{McNaughton’s index is the sum of relative abundances of the two
+#' \item 'dmn': McNaughton’s index is the sum of relative abundances of the two
 #' most abundant species of the sample (McNaughton & Wolf, 1970). Index gives
 #' values in the unit interval:
 #'
@@ -108,9 +108,9 @@
 #'
 #' where \eqn{N_1} and \eqn{N_2} are the absolute
 #' abundances of the two most dominant species and \eqn{N_{tot}} is the sum of
-#' absolute abundances of all species.}
+#' absolute abundances of all species.
 #'
-#' \item{'relative' }{ Relative index equals to the relative abundance of the
+#' \item 'relative': Relative index equals to the relative abundance of the
 #' most dominant n species of the sample (specify the number with the
 #' argument \code{ntaxa}).
 #' This index gives values in interval 0 to 1.
@@ -119,9 +119,9 @@
 #'
 #' where \eqn{N_1} is the absolute abundance of the most
 #' dominant species and \eqn{N_{tot}} is the sum of absolute abundances of all
-#' species.}
+#' species.
 #'
-#' \item{'simpson_lambda' }{ Simpson's (dominance) index or Simpson's lambda is
+#' \item 'simpson_lambda': Simpson's (dominance) index or Simpson's lambda is
 #' the sum of squared relative abundances. This index gives values in the unit interval.
 #' This value equals the probability that two randomly chosen individuals
 #' belongs to the
@@ -136,7 +136,7 @@
 #' However, this is not provided and the simpler squared sum of relative
 #' abundances is used instead as the alternative index is not in the unit
 #' interval and it is highly
-#' correlated with the simpler variant implemented here.}
+#' correlated with the simpler variant implemented here.
 #' 
 #' }
 #'
@@ -163,9 +163,9 @@
 #'
 #' @seealso
 #' \itemize{
-#'   \item{\code{\link[mia:estimateRichness]{estimateRichness}}}
-#'   \item{\code{\link[mia:estimateEvenness]{estimateEvenness}}}
-#'   \item{\code{\link[mia:estimateDiversity]{estimateDiversity}}}
+#'   \item \code{\link[mia:estimateRichness]{estimateRichness}}
+#'   \item \code{\link[mia:estimateEvenness]{estimateEvenness}}
+#'   \item \code{\link[mia:estimateDiversity]{estimateDiversity}}
 #' }
 #'
 #' @name estimateDominance
diff --git a/R/estimateEvenness.R b/R/estimateEvenness.R
index 1c7162bbb..d538d0d9c 100644
--- a/R/estimateEvenness.R
+++ b/R/estimateEvenness.R
@@ -28,8 +28,8 @@
 #'
 #' @param ... optional arguments:
 #' \itemize{
-#'   \item{threshold}{ a numeric threshold. assay values below or equal
-#'     to this threshold will be set to zero.}
+#'   \item threshold:  a numeric threshold. assay values below or equal
+#'     to this threshold will be set to zero.
 #' }
 #'
 #' @return \code{x} with additional \code{\link{colData}} named \code{*name*}
@@ -42,13 +42,13 @@
 #'
 #' The available evenness indices include the following (all in lowercase):
 #' \itemize{
-#'   \item{'camargo' }{Camargo's evenness (Camargo 1992)}
-#'   \item{'simpson_evenness' }{Simpson’s evenness is calculated as inverse Simpson diversity (1/lambda) divided by
-#'   observed species richness S: (1/lambda)/S.}
-#'   \item{'pielou' }{Pielou's evenness (Pielou, 1966), also known as Shannon or Shannon-Weaver/Wiener/Weiner
-#'     evenness; H/ln(S). The Shannon-Weaver is the preferred term; see Spellerberg and Fedor (2003).}
-#'   \item{'evar' }{Smith and Wilson’s Evar index (Smith & Wilson 1996).}
-#'   \item{'bulla' }{Bulla’s index (O) (Bulla 1994).}
+#'   \item 'camargo': Camargo's evenness (Camargo 1992)
+#'   \item 'simpson_evenness': Simpson’s evenness is calculated as inverse Simpson diversity (1/lambda) divided by
+#'   observed species richness S: (1/lambda)/S.
+#'   \item 'pielou': Pielou's evenness (Pielou, 1966), also known as Shannon or Shannon-Weaver/Wiener/Weiner
+#'     evenness; H/ln(S). The Shannon-Weaver is the preferred term; see Spellerberg and Fedor (2003).
+#'   \item 'evar': Smith and Wilson’s Evar index (Smith & Wilson 1996).
+#'   \item 'bulla': Bulla’s index (O) (Bulla 1994).
 #' }
 #'   
 #' Desirable statistical evenness metrics avoid strong bias towards very
diff --git a/R/estimateRichness.R b/R/estimateRichness.R
index 99f9c1d6d..e3635f465 100644
--- a/R/estimateRichness.R
+++ b/R/estimateRichness.R
@@ -55,7 +55,7 @@
 #'
 #' \itemize{
 #'   
-#'   \item{'ace' }{Abundance-based coverage estimator (ACE) is another
+#'   \item 'ace': Abundance-based coverage estimator (ACE) is another
 #'   nonparametric richness
 #'   index that uses sample coverage, defined based on the sum of the
 #'   probabilities
@@ -72,9 +72,9 @@
 #'   \code{\link[vegan:specpool]{estimateR}}.
 #'   For an exact formulation, see \code{\link[vegan:specpool]{estimateR}}.
 #'   Note that this index comes with an additional column with standard
-#'   error information.}
+#'   error information.
 #'   
-#'   \item{'chao1' }{This is a nonparametric estimator of species richness. It
+#'   \item 'chao1': This is a nonparametric estimator of species richness. It
 #'   assumes that rare species carry information about the (unknown) number
 #'   of unobserved species. We use here the bias-corrected version
 #'   (O'Hara 2005, Chiu et al. 2014) implemented in
@@ -85,21 +85,21 @@
 #'   This estimator uses only the singleton and doubleton counts, and
 #'   hence it gives more weight to the low abundance species.
 #'   Note that this index comes with an additional column with standard
-#'   error information.}
+#'   error information.
 #'   
-#'   \item{'hill' }{Effective species richness aka Hill index
+#'   \item 'hill': Effective species richness aka Hill index
 #'   (see e.g. Chao et al. 2016).
 #'   Currently only the case 1D is implemented. This corresponds to the exponent
 #'   of Shannon diversity. Intuitively, the effective richness indicates the
 #'   number of
 #'   species whose even distribution would lead to the same diversity than the
 #'   observed
-#'   community, where the species abundances are unevenly distributed.}
+#'   community, where the species abundances are unevenly distributed.
 #'   
-#'   \item{'observed' }{The _observed richness_ gives the number of species that
+#'   \item 'observed': The _observed richness_ gives the number of species that
 #'   is detected above a given \code{detection} threshold in the observed sample
 #'   (default 0). This is conceptually the simplest richness index. The
-#'   corresponding index in the \pkg{vegan} package is "richness".}
+#'   corresponding index in the \pkg{vegan} package is "richness".
 #'   
 #' }
 #'
@@ -129,7 +129,7 @@
 #' @seealso
 #' \code{\link[scater:plotColData]{plotColData}}
 #' \itemize{
-#'   \item{\code{\link[vegan:specpool]{estimateR}}}
+#'   \item \code{\link[vegan:specpool]{estimateR}}
 #' }
 #'
 #' @name estimateRichness
diff --git a/R/getCrossAssociation.R b/R/getCrossAssociation.R
index 1dca1b6e7..9f2ccc3be 100644
--- a/R/getCrossAssociation.R
+++ b/R/getCrossAssociation.R
@@ -100,15 +100,15 @@
 #'
 #' @param ... Additional arguments:
 #'    \itemize{
-#'        \item{\code{symmetric}}{ A single boolean value for specifying if 
+#'        \item \code{symmetric}:  A single boolean value for specifying if 
 #'        measure is symmetric or not. When \code{symmetric = TRUE}, associations
 #'        are calculated only for unique variable-pairs, and they are assigned to 
 #'        corresponding variable-pair. This decreases the number of calculations in 2-fold 
-#'        meaning faster execution. (By default: \code{symmetric = FALSE}) }
-#'        \item{\code{association_FUN}}{ A function that is used to calculate (dis-)similarity
+#'        meaning faster execution. (By default: \code{symmetric = FALSE}) 
+#'        \item \code{association_FUN}:  A function that is used to calculate (dis-)similarity
 #'        between features. Function must take matrix as an input and give numeric
 #'        values as an output. Adjust \code{method} and other parameters correspondingly.
-#'        Supported functions are, for example, \code{stats::dist} and \code{vegan::vegdist}.}
+#'        Supported functions are, for example, \code{stats::dist} and \code{vegan::vegdist}.
 #'    }
 #'    
 #' @details
diff --git a/R/importHumann.R b/R/importHumann.R
index 7c9f991d7..63336e6e5 100644
--- a/R/importHumann.R
+++ b/R/importHumann.R
@@ -10,17 +10,17 @@
 #' 
 #' @param ... additional arguments:
 #' \itemize{
-#'   \item{\code{assay.type}:} {A single character value for naming 
+#'   \item \code{assay.type}: A single character value for naming 
 #'   \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{assay}} 
-#'   (default: \code{assay.type = "counts"})}
-#'   \item{\code{removeTaxaPrefixes}:} {\code{TRUE} or \code{FALSE}: Should
+#'   (default: \code{assay.type = "counts"})
+#'   \item \code{removeTaxaPrefixes}: \code{TRUE} or \code{FALSE}: Should
 #'     taxonomic prefixes be removed? (default:
-#'     \code{removeTaxaPrefixes = FALSE})}
-#'   \item{\code{remove.suffix}:} {\code{TRUE} or \code{FALSE}: Should
+#'     \code{removeTaxaPrefixes = FALSE})
+#'   \item \code{remove.suffix}: \code{TRUE} or \code{FALSE}: Should
 #'     suffixes of sample names be removed? HUMAnN pipeline adds suffixes
 #'     to sample names. Suffixes are formed from file names. By selecting
 #'     \code{remove.suffix = TRUE}, you can remove pattern from end of sample
-#'     names that is shared by all. (default: \code{remove.suffix = FALSE})}
+#'     names that is shared by all. (default: \code{remove.suffix = FALSE})
 #' }
 #'
 #' @details
diff --git a/R/importMetaphlan.R b/R/importMetaphlan.R
index e22b91066..ee2eb4f6c 100644
--- a/R/importMetaphlan.R
+++ b/R/importMetaphlan.R
@@ -19,24 +19,24 @@
 #'   
 #' @param ... additional arguments:
 #' \itemize{
-#'   \item{\code{assay.type}:} {A single character value for naming 
+#'   \item \code{assay.type}: A single character value for naming 
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{assay}} 
-#'   (default: \code{assay.type = "counts"})}
-#'   \item{\code{assay_name}:} {A single \code{character} value for specifying which
+#'   (default: \code{assay.type = "counts"})
+#'   \item \code{assay_name}: A single \code{character} value for specifying which
 #'   assay to use for calculation. (Please use \code{assay.type} instead. 
-#'   At some point \code{assay_name} will be disabled.)}
-#'   \item{\code{removeTaxaPrefixes}:} {\code{TRUE} or \code{FALSE}: Should
+#'   At some point \code{assay_name} will be disabled.)
+#'   \item \code{removeTaxaPrefixes}: \code{TRUE} or \code{FALSE}: Should
 #'     taxonomic prefixes be removed? (default:
-#'     \code{removeTaxaPrefixes = FALSE})}
-#'   \item{\code{remove.suffix}:} {\code{TRUE} or \code{FALSE}: Should
+#'     \code{removeTaxaPrefixes = FALSE})
+#'   \item \code{remove.suffix}: \code{TRUE} or \code{FALSE}: Should
 #'     suffixes of sample names be removed? Metaphlan pipeline adds suffixes
 #'     to sample names. Suffixes are formed from file names. By selecting
 #'     \code{remove.suffix = TRUE}, you can remove pattern from end of sample
-#'     names that is shared by all. (default: \code{remove.suffix = FALSE})}
-#'   \item{\code{set.ranks}:} {\code{TRUE} or \code{FALSE}: Should the columns
+#'     names that is shared by all. (default: \code{remove.suffix = FALSE})
+#'   \item \code{set.ranks}: \code{TRUE} or \code{FALSE}: Should the columns
 #'     in the rowData that are treated as taxonomy ranks be updated according to
 #'     the ranks found in the imported data?
-#'     (default: \code{set.ranks = FALSE})}
+#'     (default: \code{set.ranks = FALSE})
 #' }
 #'
 #' @details
diff --git a/R/importQIIME2.R b/R/importQIIME2.R
index 51b2907f5..a5ca1d9ab 100644
--- a/R/importQIIME2.R
+++ b/R/importQIIME2.R
@@ -32,11 +32,11 @@
 #'
 #' @param ... additional arguments:
 #' \itemize{
-#'   \item{\code{temp}:} {the temporary directory used for decompressing the
-#'     data. (default: \code{tempdir()})}
-#'   \item{\code{removeTaxaPrefixes}:} {\code{TRUE} or \code{FALSE}: Should
+#'   \item \code{temp}: the temporary directory used for decompressing the
+#'     data. (default: \code{tempdir()})
+#'   \item \code{removeTaxaPrefixes}: \code{TRUE} or \code{FALSE}: Should
 #'     taxonomic prefixes be removed? (default:
-#'     \code{removeTaxaPrefixes = FALSE})}
+#'     \code{removeTaxaPrefixes = FALSE})
 #' }
 #'
 #' @details
diff --git a/R/makeTreeSummarizedExperimentFromBiom.R b/R/makeTreeSummarizedExperimentFromBiom.R
index 4a62c0a2f..33116fb46 100644
--- a/R/makeTreeSummarizedExperimentFromBiom.R
+++ b/R/makeTreeSummarizedExperimentFromBiom.R
@@ -21,9 +21,9 @@
 #' 
 #' @param ... additional arguments 
 #'   \itemize{
-#'        \item{\code{patter}}{\code{character} value specifying artifacts
+#'        \item \code{patter}: \code{character} value specifying artifacts
 #'        to be removed. If \code{patterns = "auto"}, special characters
-#'        are removed. (default: \code{pattern = "auto"})}
+#'        are removed. (default: \code{pattern = "auto"})
 #'    }
 #' 
 #' @return An object of class
diff --git a/R/meltAssay.R b/R/meltAssay.R
index 63ac990a0..53bc99118 100644
--- a/R/meltAssay.R
+++ b/R/meltAssay.R
@@ -46,10 +46,10 @@
 #'
 #' @param ... optional arguments:
 #' \itemize{
-#'   \item{check_names}{ A boolean value passed to data.frame function's check.name
+#'   \item check_names: A boolean value passed to data.frame function's check.name
 #'   argument. Determines if sample names are checked that they are syntactically 
 #'   valid variable names and are not duplicated. If they are not, sample names 
-#'   are modified. (default: \code{check_names = TRUE})}
+#'   are modified. (default: \code{check_names = TRUE})
 #' }
 #'
 #' @return A \code{tibble} with the molten data. The assay values are given in a
diff --git a/R/taxonomy.R b/R/taxonomy.R
index 51d2435a1..c14261607 100644
--- a/R/taxonomy.R
+++ b/R/taxonomy.R
@@ -57,10 +57,10 @@
 #'
 #' @param from 
 #' \itemize{
-#'   \item{For \code{mapTaxonomy}: }{a scalar \code{character} value, which 
-#'     must be a valid taxonomic rank. (default: \code{NULL})}
-#'   \item{otherwise a \code{Taxa} object as returned by 
-#'     \code{\link[DECIPHER:IdTaxa]{IdTaxa}}}
+#'   \item For \code{mapTaxonomy}: a scalar \code{character} value, which 
+#'     must be a valid taxonomic rank. (default: \code{NULL})
+#'   \item otherwise a \code{Taxa} object as returned by 
+#'     \code{\link[DECIPHER:IdTaxa]{IdTaxa}}
 #' }
 #'
 #' @param to a scalar \code{character} value, which must be a valid 
@@ -83,13 +83,13 @@
 #'
 #' @return
 #' \itemize{
-#'   \item{\code{taxonomyRanks}:} {a \code{character} vector with all the
-#'     taxonomic ranks found in \code{colnames(rowData(x))}}
-#'   \item{\code{taxonomyRankEmpty}:} {a \code{logical} value}
-#'   \item{\code{mapTaxonomy}:} {a \code{list} per element of taxa. Each 
+#'   \item \code{taxonomyRanks}: a \code{character} vector with all the
+#'     taxonomic ranks found in \code{colnames(rowData(x))}
+#'   \item \code{taxonomyRankEmpty}: a \code{logical} value
+#'   \item \code{mapTaxonomy}: a \code{list} per element of taxa. Each 
 #'     element is either a \code{DataFrame}, a \code{character} or \code{NULL}.
 #'     If all \code{character} results have the length of one, a single 
-#'     \code{character} vector is returned.}
+#'     \code{character} vector is returned.
 #' }
 #'
 #' @name taxonomy-methods
@@ -433,11 +433,11 @@ setMethod("getTaxonomyLabels", signature = c(x = "SummarizedExperiment"),
 #' 
 #' @return
 #' \itemize{
-#'   \item{\code{addHierarchyTree}:} {a \code{TreeSummarizedExperiment} whose
+#'   \item \code{addHierarchyTree}: a \code{TreeSummarizedExperiment} whose
 #'   \code{phylo} tree represents the hierarchy among available taxonomy 
-#'   information}
-#'   \item{\code{getHierarchyTree}:} {a \code{phylo} tree representing the 
-#'   hierarchy among available taxonomy information.}
+#'   information.
+#'   \item \code{getHierarchyTree}: a \code{phylo} tree representing the 
+#'   hierarchy among available taxonomy information.
 #' }
 #' 
 #' @name hierarchy-tree
diff --git a/R/transformCounts.R b/R/transformCounts.R
index bb5d40b8a..4cd39f3f0 100644
--- a/R/transformCounts.R
+++ b/R/transformCounts.R
@@ -33,9 +33,9 @@
 #'
 #' @param ... additional arguments passed on to \code{vegan:decostand}:
 #' \itemize{
-#'   \item{\code{ref_vals}:} {A single value which will be used to fill 
+#'   \item \code{ref_vals}: A single value which will be used to fill 
 #'   reference sample's column in returned assay when calculating alr. 
-#'   (default: \code{ref_vals = NA})}
+#'   (default: \code{ref_vals = NA})
 #' }
 #' @details
 #'
@@ -52,63 +52,63 @@
 #'
 #' \itemize{
 #' 
-#' \item{'alr'}{ Additive log ratio (alr) transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'alr': Additive log ratio (alr) transformation, please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'chi.square'}{ Chi square transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'chi.square': Chi square transformation, please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'clr'}{ Centered log ratio (clr) transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'clr': Centered log ratio (clr) transformation, please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #'
-#' \item{'frequency'}{ Frequency transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'frequency': Frequency transformation, please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'hellinger'}{ Hellinger transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'hellinger':  Hellinger transformation, please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'log'}{ Logarithmic transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'log':  Logarithmic transformation, please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'log10'}{ log10 transformation can be used for reducing the skewness
+#' \item 'log10': log10 transformation can be used for reducing the skewness
 #' of the data.
 #' \deqn{log10 = \log_{10} x}{%
 #' log10 = log10(x)}
-#' where \eqn{x} is a single value of data.}
+#' where \eqn{x} is a single value of data.
 #' 
-#' \item{'log2'}{ log2 transformation can be used for reducing the skewness of
+#' \item 'log2': log2 transformation can be used for reducing the skewness of
 #' the data.
 #' \deqn{log2 = \log_{2} x}{%
 #' log2 = log2(x)}
-#' where \eqn{x} is a single value of data.}
+#' where \eqn{x} is a single value of data.
 #' 
-#' \item{'normalize'}{ Make margin sum of squares equal to one. Please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'normalize': Make margin sum of squares equal to one. Please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'pa'}{ Transforms table to presence/absence table. Please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'pa': Transforms table to presence/absence table. Please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #'
-#' \item{'rank'}{ Rank transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'rank': Rank transformation, please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'rclr'}{ Robust clr transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'rclr':  Robust clr transformation, please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'relabundance'}{ Relative transformation (alias for 'total'), please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'relabundance': Relative transformation (alias for 'total'), please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'rrank'}{ Relative rank transformation, please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'rrank': Relative rank transformation, please refer to 
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'standardize'}{ Scale 'x' to zero mean and unit variance (alias for
-#' 'z'), please refer to \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'standardize': Scale 'x' to zero mean and unit variance (alias for
+#' 'z'), please refer to \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'total'}{ Divide by margin total (alias for
+#' \item 'total': Divide by margin total (alias for
 #' 'relabundance'), please refer to 
-#' \code{\link[vegan:decostand]{decostand}} for details.}
+#' \code{\link[vegan:decostand]{decostand}} for details.
 #' 
-#' \item{'z'}{ Z transformation (alias for 'standardize'),
-#' please refer to \code{\link[vegan:decostand]{decostand}} for details.}
+#' \item 'z': Z transformation (alias for 'standardize'),
+#' please refer to \code{\link[vegan:decostand]{decostand}} for details.
 #'
 #' }
 #'
diff --git a/man/agglomerate-methods.Rd b/man/agglomerate-methods.Rd
index 04909b067..d33fd0e23 100644
--- a/man/agglomerate-methods.Rd
+++ b/man/agglomerate-methods.Rd
@@ -67,20 +67,20 @@ to \code{\link[=agglomerate-methods]{agglomerateByVariable}} and
 to \code{getPrevalence} and \code{getPrevalentTaxa} and used in
 \code{agglomeratebyPrevalence}
 \itemize{
-\item{\code{remove_empty_ranks}}{A single boolean value for selecting
+\item \code{remove_empty_ranks}: A single boolean value for selecting
 whether to remove those columns of rowData that include only NAs after
-agglomeration. (By default: \code{remove_empty_ranks = FALSE})}
-\item{\code{make_unique}}{A single boolean value for selecting
-whether to make rownames unique. (By default: \code{make_unique = TRUE})}
-\item{\code{detection}}{Detection threshold for absence/presence.
+agglomeration. (By default: \code{remove_empty_ranks = FALSE})
+\item \code{make_unique}: A single boolean value for selecting
+whether to make rownames unique. (By default: \code{make_unique = TRUE})
+\item \code{detection}: Detection threshold for absence/presence.
 Either an absolute value compared directly to the values of \code{x}
-or a relative value between 0 and 1, if \code{as_relative = FALSE}.}
-\item{\code{prevalence}}{Prevalence threshold (in 0 to 1). The
+or a relative value between 0 and 1, if \code{as_relative = FALSE}.
+\item \code{prevalence}: Prevalence threshold (in 0 to 1). The
 required prevalence is strictly greater by default. To include the
-limit, set \code{include_lowest} to \code{TRUE}.}
-\item{\code{as.relative}}{Logical scalar: Should the detection
+limit, set \code{include_lowest} to \code{TRUE}.
+\item \code{as.relative}: Logical scalar: Should the detection
 threshold be applied on compositional (relative) abundances?
-(default: \code{FALSE})}
+(default: \code{FALSE})
 }}
 
 \item{rank}{a single character defining a taxonomic rank. Must be a value of
diff --git a/man/estimateDiversity.Rd b/man/estimateDiversity.Rd
index dba7006f4..4180e0548 100644
--- a/man/estimateDiversity.Rd
+++ b/man/estimateDiversity.Rd
@@ -91,20 +91,20 @@ indices.}
 
 \item{...}{optional arguments:
 \itemize{
-\item{threshold}{ A numeric value in the unit interval,
+\item threshold: A numeric value in the unit interval,
 determining the threshold for coverage index. By default,
-\code{threshold} is 0.9.}
-\item{quantile}{ Arithmetic abundance classes are evenly cut up to to
+\code{threshold} is 0.9.
+\item quantile: Arithmetic abundance classes are evenly cut up to to
 this quantile of the data. The assumption is that abundances higher than
 this are not common, and they are classified in their own group.
-By default, \code{quantile} is 0.5.}
-\item{num_of_classes}{ The number of arithmetic abundance classes
+By default, \code{quantile} is 0.5.
+\item num_of_classes: The number of arithmetic abundance classes
 from zero to the quantile cutoff indicated by \code{quantile}.
-By default, \code{num_of_classes} is 50.}
-\item{only.tips}{ A boolean value specifying whether to remove internal
+By default, \code{num_of_classes} is 50.
+\item only.tips: A boolean value specifying whether to remove internal
 nodes when Faith's index is calculated. When \code{only.tips=TRUE}, those
 rows that are not tips of tree are removed.
-(By default: \code{only.tips=FALSE})}
+(By default: \code{only.tips=FALSE})
 }}
 
 \item{BPPARAM}{A
@@ -146,11 +146,11 @@ By default, this function returns all indices.
 
 \itemize{
 
-\item{'coverage' }{Number of species needed to cover a given fraction of
+\item 'coverage': Number of species needed to cover a given fraction of
 the ecosystem (50 percent by default). Tune this with the threshold
-argument.}
+argument.
 
-\item{'faith' }{Faith's phylogenetic alpha diversity index measures how
+\item 'faith': Faith's phylogenetic alpha diversity index measures how
 long the taxonomic distance is between taxa that are present in the sample.
 Larger values represent higher diversity. Using this index requires
 rowTree. (Faith 1992)
@@ -159,12 +159,12 @@ If the data includes features that are not in tree's tips but in
 internal nodes, there are two options. First, you can keep those features,
 and prune the tree to match features so that each tip can be found from
 the features. Other option is to remove all features that are not tips.
-(See \code{only.tips} parameter)}
+(See \code{only.tips} parameter)
 
-\item{'fisher' }{Fisher's alpha; as implemented in
-\code{\link[vegan:diversity]{vegan::fisher.alpha}}. (Fisher et al. 1943)}
+\item 'fisher': Fisher's alpha; as implemented in
+\code{\link[vegan:diversity]{vegan::fisher.alpha}}. (Fisher et al. 1943)
 
-\item{'gini_simpson' }{Gini-Simpson diversity i.e. \eqn{1 - lambda},
+\item 'gini_simpson': Gini-Simpson diversity i.e. \eqn{1 - lambda},
 where \eqn{lambda} is the
 Simpson index, calculated as the sum of squared relative abundances.
 This corresponds to the diversity index
@@ -173,25 +173,25 @@ This is also called Gibbs–Martin, or Blau index in sociology,
 psychology and management studies. The Gini-Simpson index (1-lambda)
 should not be
 confused with Simpson's dominance (lambda), Gini index, or
-inverse Simpson index (1/lambda).}
+inverse Simpson index (1/lambda).
 
-\item{'inverse_simpson' }{Inverse Simpson diversity:
+\item 'inverse_simpson': Inverse Simpson diversity:
 \eqn{1/lambda} where \eqn{lambda=sum(p^2)} and p refers to relative
 abundances.
 This corresponds to the diversity index
 'invsimpson' in vegan::diversity. Don't confuse this with the
-closely related Gini-Simpson index}
+closely related Gini-Simpson index
 
-\item{'log_modulo_skewness' }{The rarity index characterizes the
+\item 'log_modulo_skewness': The rarity index characterizes the
 concentration of species at low abundance. Here, we use the skewness of
 the frequency
 distribution of arithmetic abundance classes (see Magurran & McGill 2011).
 These are typically right-skewed; to avoid taking log of occasional
 negative skews, we follow Locey & Lennon (2016) and use the log-modulo
 transformation that adds a value of one to each measure of skewness to
-allow logarithmization.}
+allow logarithmization.
 
-\item{'shannon' }{Shannon diversity (entropy).}
+\item 'shannon': Shannon diversity (entropy).
 
 }
 }
@@ -290,11 +290,11 @@ A Consumer's Guide to Diversity Indices.
 \seealso{
 \code{\link[scater:plotColData]{plotColData}}
 \itemize{
-\item{\code{\link[mia:estimateRichness]{estimateRichness}}}
-\item{\code{\link[mia:estimateEvenness]{estimateEvenness}}}
-\item{\code{\link[mia:estimateDominance]{estimateDominance}}}
-\item{\code{\link[vegan:diversity]{diversity}}}
-\item{\code{\link[vegan:specpool]{estimateR}}}
+\item \code{\link[mia:estimateRichness]{estimateRichness}}
+\item \code{\link[mia:estimateEvenness]{estimateEvenness}}
+\item \code{\link[mia:estimateDominance]{estimateDominance}}
+\item \code{\link[vegan:diversity]{diversity}}
+\item \code{\link[vegan:specpool]{estimateR}}
 }
 }
 \author{
diff --git a/man/estimateDominance.Rd b/man/estimateDominance.Rd
index b53304c8f..72176cfb5 100644
--- a/man/estimateDominance.Rd
+++ b/man/estimateDominance.Rd
@@ -96,11 +96,11 @@ indices:
 
 \itemize{
 
-\item{'absolute' }{Absolute index equals to the absolute abundance of the
+\item 'absolute': Absolute index equals to the absolute abundance of the
 most dominant n species of the sample (specify the number with the argument
-\code{ntaxa}). Index gives positive integer values.}
+\code{ntaxa}). Index gives positive integer values.
 
-\item{'dbp' }{Berger-Parker index (See Berger & Parker 1970) calculation
+\item 'dbp': Berger-Parker index (See Berger & Parker 1970) calculation
 is a special case of the 'relative' index. dbp is the relative abundance of
 the most
 abundant species of the sample. Index gives values in interval 0 to 1,
@@ -109,9 +109,9 @@ where bigger value represent greater dominance.
 \deqn{dbp = \frac{N_1}{N_{tot}}}{%
 dbp = N_1/N_tot} where \eqn{N_1} is the absolute abundance of the most
 dominant species and \eqn{N_{tot}} is the sum of absolute abundances of all
-species.}
+species.
 
-\item{'core_abundance' }{ Core abundance index is related to core species.
+\item 'core_abundance': Core abundance index is related to core species.
 Core species are species that are most abundant in all samples, i.e., in
 whole data set. Core species are defined as those species that have
 prevalence over 50\\%. It means that in order to belong to core species,
@@ -123,9 +123,9 @@ abundances of core species in the sample. Index gives values in interval
 \deqn{core_abundance = \frac{N_{core}}{N_{tot}}}{%
 core_abundance = N_core/N_tot} where \eqn{N_{core}} is the sum of absolute
 abundance of the core species and \eqn{N_{tot}} is the sum of absolute
-abundances of all species.}
+abundances of all species.
 
-\item{'gini' }{ Gini index is probably best-known from socio-economic
+\item 'gini':  Gini index is probably best-known from socio-economic
 contexts (Gini 1921). In economics, it is used to measure, for example, how
 unevenly income is distributed among population. Here, Gini index is used
 similarly, but income is replaced with abundance.
@@ -134,9 +134,9 @@ If there is small group of species
 that represent large portion of total abundance of microbes, the inequality
 is large and Gini index closer to 1. If all species has equally large
 abundances, the equality is perfect and Gini index equals 0. This index
-should not be confused with Gini-Simpson index, which quantifies diversity.}
+should not be confused with Gini-Simpson index, which quantifies diversity.
 
-\item{'dmn' }{McNaughton’s index is the sum of relative abundances of the two
+\item 'dmn': McNaughton’s index is the sum of relative abundances of the two
 most abundant species of the sample (McNaughton & Wolf, 1970). Index gives
 values in the unit interval:
 
@@ -144,9 +144,9 @@ values in the unit interval:
 
 where \eqn{N_1} and \eqn{N_2} are the absolute
 abundances of the two most dominant species and \eqn{N_{tot}} is the sum of
-absolute abundances of all species.}
+absolute abundances of all species.
 
-\item{'relative' }{ Relative index equals to the relative abundance of the
+\item 'relative': Relative index equals to the relative abundance of the
 most dominant n species of the sample (specify the number with the
 argument \code{ntaxa}).
 This index gives values in interval 0 to 1.
@@ -155,9 +155,9 @@ This index gives values in interval 0 to 1.
 
 where \eqn{N_1} is the absolute abundance of the most
 dominant species and \eqn{N_{tot}} is the sum of absolute abundances of all
-species.}
+species.
 
-\item{'simpson_lambda' }{ Simpson's (dominance) index or Simpson's lambda is
+\item 'simpson_lambda': Simpson's (dominance) index or Simpson's lambda is
 the sum of squared relative abundances. This index gives values in the unit interval.
 This value equals the probability that two randomly chosen individuals
 belongs to the
@@ -172,7 +172,7 @@ There is also a more advanced Simpson dominance index (Simpson 1949).
 However, this is not provided and the simpler squared sum of relative
 abundances is used instead as the alternative index is not in the unit
 interval and it is highly
-correlated with the simpler variant implemented here.}
+correlated with the simpler variant implemented here.
 
 }
 }
@@ -238,9 +238,9 @@ Measurement of Diversity.
 }
 \seealso{
 \itemize{
-\item{\code{\link[mia:estimateRichness]{estimateRichness}}}
-\item{\code{\link[mia:estimateEvenness]{estimateEvenness}}}
-\item{\code{\link[mia:estimateDiversity]{estimateDiversity}}}
+\item \code{\link[mia:estimateRichness]{estimateRichness}}
+\item \code{\link[mia:estimateEvenness]{estimateEvenness}}
+\item \code{\link[mia:estimateDiversity]{estimateDiversity}}
 }
 }
 \author{
diff --git a/man/estimateEvenness.Rd b/man/estimateEvenness.Rd
index 4a08c768c..50ae9bba6 100644
--- a/man/estimateEvenness.Rd
+++ b/man/estimateEvenness.Rd
@@ -44,8 +44,8 @@ stored in.}
 
 \item{...}{optional arguments:
 \itemize{
-\item{threshold}{ a numeric threshold. assay values below or equal
-to this threshold will be set to zero.}
+\item threshold:  a numeric threshold. assay values below or equal
+to this threshold will be set to zero.
 }}
 
 \item{BPPARAM}{A
@@ -69,13 +69,13 @@ By default, this function returns all indices.
 
 The available evenness indices include the following (all in lowercase):
 \itemize{
-\item{'camargo' }{Camargo's evenness (Camargo 1992)}
-\item{'simpson_evenness' }{Simpson’s evenness is calculated as inverse Simpson diversity (1/lambda) divided by
-observed species richness S: (1/lambda)/S.}
-\item{'pielou' }{Pielou's evenness (Pielou, 1966), also known as Shannon or Shannon-Weaver/Wiener/Weiner
-evenness; H/ln(S). The Shannon-Weaver is the preferred term; see Spellerberg and Fedor (2003).}
-\item{'evar' }{Smith and Wilson’s Evar index (Smith & Wilson 1996).}
-\item{'bulla' }{Bulla’s index (O) (Bulla 1994).}
+\item 'camargo': Camargo's evenness (Camargo 1992)
+\item 'simpson_evenness': Simpson’s evenness is calculated as inverse Simpson diversity (1/lambda) divided by
+observed species richness S: (1/lambda)/S.
+\item 'pielou': Pielou's evenness (Pielou, 1966), also known as Shannon or Shannon-Weaver/Wiener/Weiner
+evenness; H/ln(S). The Shannon-Weaver is the preferred term; see Spellerberg and Fedor (2003).
+\item 'evar': Smith and Wilson’s Evar index (Smith & Wilson 1996).
+\item 'bulla': Bulla’s index (O) (Bulla 1994).
 }
 
 Desirable statistical evenness metrics avoid strong bias towards very
diff --git a/man/estimateRichness.Rd b/man/estimateRichness.Rd
index 2073d4c1f..aa9317496 100644
--- a/man/estimateRichness.Rd
+++ b/man/estimateRichness.Rd
@@ -84,7 +84,7 @@ The following richness indices are provided.
 
 \itemize{
 
-\item{'ace' }{Abundance-based coverage estimator (ACE) is another
+\item 'ace': Abundance-based coverage estimator (ACE) is another
 nonparametric richness
 index that uses sample coverage, defined based on the sum of the
 probabilities
@@ -101,9 +101,9 @@ exact abundance. We use here the bias-corrected version
 \code{\link[vegan:specpool]{estimateR}}.
 For an exact formulation, see \code{\link[vegan:specpool]{estimateR}}.
 Note that this index comes with an additional column with standard
-error information.}
+error information.
 
-\item{'chao1' }{This is a nonparametric estimator of species richness. It
+\item 'chao1': This is a nonparametric estimator of species richness. It
 assumes that rare species carry information about the (unknown) number
 of unobserved species. We use here the bias-corrected version
 (O'Hara 2005, Chiu et al. 2014) implemented in
@@ -114,21 +114,21 @@ for an exact formulation, see \code{\link[vegan:specpool]{estimateR}}.
 This estimator uses only the singleton and doubleton counts, and
 hence it gives more weight to the low abundance species.
 Note that this index comes with an additional column with standard
-error information.}
+error information.
 
-\item{'hill' }{Effective species richness aka Hill index
+\item 'hill': Effective species richness aka Hill index
 (see e.g. Chao et al. 2016).
 Currently only the case 1D is implemented. This corresponds to the exponent
 of Shannon diversity. Intuitively, the effective richness indicates the
 number of
 species whose even distribution would lead to the same diversity than the
 observed
-community, where the species abundances are unevenly distributed.}
+community, where the species abundances are unevenly distributed.
 
-\item{'observed' }{The \emph{observed richness} gives the number of species that
+\item 'observed': The \emph{observed richness} gives the number of species that
 is detected above a given \code{detection} threshold in the observed sample
 (default 0). This is conceptually the simplest richness index. The
-corresponding index in the \pkg{vegan} package is "richness".}
+corresponding index in the \pkg{vegan} package is "richness".
 
 }
 }
@@ -214,7 +214,7 @@ Species richness estimators: how many species can dance on the head of a pin?
 \seealso{
 \code{\link[scater:plotColData]{plotColData}}
 \itemize{
-\item{\code{\link[vegan:specpool]{estimateR}}}
+\item \code{\link[vegan:specpool]{estimateR}}
 }
 }
 \author{
diff --git a/man/getCrossAssociation.Rd b/man/getCrossAssociation.Rd
index 963d73264..179f32866 100644
--- a/man/getCrossAssociation.Rd
+++ b/man/getCrossAssociation.Rd
@@ -45,15 +45,15 @@ object.}
 
 \item{...}{Additional arguments:
 \itemize{
-\item{\code{symmetric}}{ A single boolean value for specifying if
+\item \code{symmetric}:  A single boolean value for specifying if
 measure is symmetric or not. When \code{symmetric = TRUE}, associations
 are calculated only for unique variable-pairs, and they are assigned to
 corresponding variable-pair. This decreases the number of calculations in 2-fold
-meaning faster execution. (By default: \code{symmetric = FALSE}) }
-\item{\code{association_FUN}}{ A function that is used to calculate (dis-)similarity
+meaning faster execution. (By default: \code{symmetric = FALSE})
+\item \code{association_FUN}:  A function that is used to calculate (dis-)similarity
 between features. Function must take matrix as an input and give numeric
 values as an output. Adjust \code{method} and other parameters correspondingly.
-Supported functions are, for example, \code{stats::dist} and \code{vegan::vegdist}.}
+Supported functions are, for example, \code{stats::dist} and \code{vegan::vegdist}.
 }}
 
 \item{experiment1}{A single character or numeric value for selecting the experiment 1
diff --git a/man/hierarchy-tree.Rd b/man/hierarchy-tree.Rd
index b05e6eec0..c13d45f03 100644
--- a/man/hierarchy-tree.Rd
+++ b/man/hierarchy-tree.Rd
@@ -25,11 +25,11 @@ object}
 }
 \value{
 \itemize{
-\item{\code{addHierarchyTree}:} {a \code{TreeSummarizedExperiment} whose
+\item \code{addHierarchyTree}: a \code{TreeSummarizedExperiment} whose
 \code{phylo} tree represents the hierarchy among available taxonomy
-information}
-\item{\code{getHierarchyTree}:} {a \code{phylo} tree representing the
-hierarchy among available taxonomy information.}
+information.
+\item \code{getHierarchyTree}: a \code{phylo} tree representing the
+hierarchy among available taxonomy information.
 }
 }
 \description{
diff --git a/man/importHUMAnN.Rd b/man/importHUMAnN.Rd
index 64d31b09c..49e03660c 100644
--- a/man/importHUMAnN.Rd
+++ b/man/importHUMAnN.Rd
@@ -14,17 +14,17 @@ path of the sample metadata file. The file must be in \code{tsv} format
 
 \item{...}{additional arguments:
 \itemize{
-\item{\code{assay.type}:} {A single character value for naming
+\item \code{assay.type}: A single character value for naming
 \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{assay}}
-(default: \code{assay.type = "counts"})}
-\item{\code{removeTaxaPrefixes}:} {\code{TRUE} or \code{FALSE}: Should
+(default: \code{assay.type = "counts"})
+\item \code{removeTaxaPrefixes}: \code{TRUE} or \code{FALSE}: Should
 taxonomic prefixes be removed? (default:
-\code{removeTaxaPrefixes = FALSE})}
-\item{\code{remove.suffix}:} {\code{TRUE} or \code{FALSE}: Should
+\code{removeTaxaPrefixes = FALSE})
+\item \code{remove.suffix}: \code{TRUE} or \code{FALSE}: Should
 suffixes of sample names be removed? HUMAnN pipeline adds suffixes
 to sample names. Suffixes are formed from file names. By selecting
 \code{remove.suffix = TRUE}, you can remove pattern from end of sample
-names that is shared by all. (default: \code{remove.suffix = FALSE})}
+names that is shared by all. (default: \code{remove.suffix = FALSE})
 }}
 }
 \value{
diff --git a/man/importMetaPhlAn.Rd b/man/importMetaPhlAn.Rd
index 0bf7a0e08..c94920ca0 100644
--- a/man/importMetaPhlAn.Rd
+++ b/man/importMetaPhlAn.Rd
@@ -23,24 +23,24 @@ path of the phylogenetic tree.
 
 \item{...}{additional arguments:
 \itemize{
-\item{\code{assay.type}:} {A single character value for naming
+\item \code{assay.type}: A single character value for naming
 \code{\link[SummarizedExperiment:SummarizedExperiment-class]{assay}}
-(default: \code{assay.type = "counts"})}
-\item{\code{assay_name}:} {A single \code{character} value for specifying which
+(default: \code{assay.type = "counts"})
+\item \code{assay_name}: A single \code{character} value for specifying which
 assay to use for calculation. (Please use \code{assay.type} instead.
-At some point \code{assay_name} will be disabled.)}
-\item{\code{removeTaxaPrefixes}:} {\code{TRUE} or \code{FALSE}: Should
+At some point \code{assay_name} will be disabled.)
+\item \code{removeTaxaPrefixes}: \code{TRUE} or \code{FALSE}: Should
 taxonomic prefixes be removed? (default:
-\code{removeTaxaPrefixes = FALSE})}
-\item{\code{remove.suffix}:} {\code{TRUE} or \code{FALSE}: Should
+\code{removeTaxaPrefixes = FALSE})
+\item \code{remove.suffix}: \code{TRUE} or \code{FALSE}: Should
 suffixes of sample names be removed? Metaphlan pipeline adds suffixes
 to sample names. Suffixes are formed from file names. By selecting
 \code{remove.suffix = TRUE}, you can remove pattern from end of sample
-names that is shared by all. (default: \code{remove.suffix = FALSE})}
-\item{\code{set.ranks}:} {\code{TRUE} or \code{FALSE}: Should the columns
+names that is shared by all. (default: \code{remove.suffix = FALSE})
+\item \code{set.ranks}: \code{TRUE} or \code{FALSE}: Should the columns
 in the rowData that are treated as taxonomy ranks be updated according to
 the ranks found in the imported data?
-(default: \code{set.ranks = FALSE})}
+(default: \code{set.ranks = FALSE})
 }}
 }
 \value{
diff --git a/man/importQIIME2.Rd b/man/importQIIME2.Rd
index 45285ed29..7ece59bcd 100644
--- a/man/importQIIME2.Rd
+++ b/man/importQIIME2.Rd
@@ -44,11 +44,11 @@ the phylogenetic tree. (default: \code{phyTreeFile = NULL}).}
 
 \item{...}{additional arguments:
 \itemize{
-\item{\code{temp}:} {the temporary directory used for decompressing the
-data. (default: \code{tempdir()})}
-\item{\code{removeTaxaPrefixes}:} {\code{TRUE} or \code{FALSE}: Should
+\item \code{temp}: the temporary directory used for decompressing the
+data. (default: \code{tempdir()})
+\item \code{removeTaxaPrefixes}: \code{TRUE} or \code{FALSE}: Should
 taxonomic prefixes be removed? (default:
-\code{removeTaxaPrefixes = FALSE})}
+\code{removeTaxaPrefixes = FALSE})
 }}
 
 \item{file}{character, path of the input qza file. Only files in format of
diff --git a/man/isContaminant.Rd b/man/isContaminant.Rd
index 08b2cf1fc..95b6a74b7 100644
--- a/man/isContaminant.Rd
+++ b/man/isContaminant.Rd
@@ -80,11 +80,11 @@ as batch information. (default: \code{batch = NULL})}
 \code{\link[decontam:isNotContaminant]{decontam:isNotContaminant}}}
 
 \item{...}{\itemize{
-\item{for \code{isContaminant}/ \code{isNotContaminant}: }{arguments
+\item for \code{isContaminant}/ \code{isNotContaminant}: arguments
 passed on to \code{\link[decontam:isContaminant]{decontam:isContaminant}}
-or \code{\link[decontam:isNotContaminant]{decontam:isNotContaminant}}}
-\item{for \code{addContaminantQC}/\code{addNotContaminantQC}: }{arguments
-passed on to \code{isContaminant}/ \code{isNotContaminant}}
+or \code{\link[decontam:isNotContaminant]{decontam:isNotContaminant}}
+\item for \code{addContaminantQC}/\code{addNotContaminantQC}: arguments
+passed on to \code{isContaminant}/ \code{isNotContaminant}
 }}
 }
 \value{
diff --git a/man/makeTreeSEFromBiom.Rd b/man/makeTreeSEFromBiom.Rd
index 1cb1115cd..8b7ab99f3 100644
--- a/man/makeTreeSEFromBiom.Rd
+++ b/man/makeTreeSEFromBiom.Rd
@@ -23,9 +23,9 @@ makeTreeSummarizedExperimentFromBiom(obj, ...)
 
 \item{...}{additional arguments
 \itemize{
-\item{\code{patter}}{\code{character} value specifying artifacts
+\item \code{patter}: \code{character} value specifying artifacts
 to be removed. If \code{patterns = "auto"}, special characters
-are removed. (default: \code{pattern = "auto"})}
+are removed. (default: \code{pattern = "auto"})
 }}
 
 \item{obj}{object of type \code{\link[biomformat:read_biom]{biom}}}
diff --git a/man/meltAssay.Rd b/man/meltAssay.Rd
index 85aded844..c73cf78a3 100644
--- a/man/meltAssay.Rd
+++ b/man/meltAssay.Rd
@@ -64,10 +64,10 @@ for the sample identifier. (default: \code{sample_name = "SampleID"})}
 
 \item{...}{optional arguments:
 \itemize{
-\item{check_names}{ A boolean value passed to data.frame function's check.name
+\item check_names: A boolean value passed to data.frame function's check.name
 argument. Determines if sample names are checked that they are syntactically
 valid variable names and are not duplicated. If they are not, sample names
-are modified. (default: \code{check_names = TRUE})}
+are modified. (default: \code{check_names = TRUE})
 }}
 }
 \value{
diff --git a/man/taxonomy-methods.Rd b/man/taxonomy-methods.Rd
index 87b0b894a..3c92e9bf7 100644
--- a/man/taxonomy-methods.Rd
+++ b/man/taxonomy-methods.Rd
@@ -98,10 +98,10 @@ taxonomic information. If no information is found,\code{NULL} is returned
 for the individual element. (default: \code{NULL})}
 
 \item{from}{\itemize{
-\item{For \code{mapTaxonomy}: }{a scalar \code{character} value, which
-must be a valid taxonomic rank. (default: \code{NULL})}
-\item{otherwise a \code{Taxa} object as returned by
-\code{\link[DECIPHER:IdTaxa]{IdTaxa}}}
+\item For \code{mapTaxonomy}: a scalar \code{character} value, which
+must be a valid taxonomic rank. (default: \code{NULL})
+\item otherwise a \code{Taxa} object as returned by
+\code{\link[DECIPHER:IdTaxa]{IdTaxa}}
 }}
 
 \item{to}{a scalar \code{character} value, which must be a valid
@@ -113,13 +113,13 @@ taxonomic rank. (default: \code{NULL})}
 }
 \value{
 \itemize{
-\item{\code{taxonomyRanks}:} {a \code{character} vector with all the
-taxonomic ranks found in \code{colnames(rowData(x))}}
-\item{\code{taxonomyRankEmpty}:} {a \code{logical} value}
-\item{\code{mapTaxonomy}:} {a \code{list} per element of taxa. Each
+\item \code{taxonomyRanks}: a \code{character} vector with all the
+taxonomic ranks found in \code{colnames(rowData(x))}
+\item \code{taxonomyRankEmpty}: a \code{logical} value
+\item \code{mapTaxonomy}: a \code{list} per element of taxa. Each
 element is either a \code{DataFrame}, a \code{character} or \code{NULL}.
 If all \code{character} results have the length of one, a single
-\code{character} vector is returned.}
+\code{character} vector is returned.
 }
 }
 \description{
diff --git a/man/transformAssay.Rd b/man/transformAssay.Rd
index f49a71e98..18e069f16 100644
--- a/man/transformAssay.Rd
+++ b/man/transformAssay.Rd
@@ -115,9 +115,9 @@ abundance table.}
 
 \item{...}{additional arguments passed on to \code{vegan:decostand}:
 \itemize{
-\item{\code{ref_vals}:} {A single value which will be used to fill
+\item \code{ref_vals}: A single value which will be used to fill
 reference sample's column in returned assay when calculating alr.
-(default: \code{ref_vals = NA})}
+(default: \code{ref_vals = NA})
 }}
 
 \item{pseudocount}{TRUE, FALSE, or a numeric value. When TRUE,
@@ -151,63 +151,63 @@ The available transformation methods include:
 
 \itemize{
 
-\item{'alr'}{ Additive log ratio (alr) transformation, please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'alr': Additive log ratio (alr) transformation, please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'chi.square'}{ Chi square transformation, please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'chi.square': Chi square transformation, please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'clr'}{ Centered log ratio (clr) transformation, please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'clr': Centered log ratio (clr) transformation, please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'frequency'}{ Frequency transformation, please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'frequency': Frequency transformation, please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'hellinger'}{ Hellinger transformation, please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'hellinger':  Hellinger transformation, please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'log'}{ Logarithmic transformation, please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'log':  Logarithmic transformation, please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'log10'}{ log10 transformation can be used for reducing the skewness
+\item 'log10': log10 transformation can be used for reducing the skewness
 of the data.
 \deqn{log10 = \log_{10} x}{%
 log10 = log10(x)}
-where \eqn{x} is a single value of data.}
+where \eqn{x} is a single value of data.
 
-\item{'log2'}{ log2 transformation can be used for reducing the skewness of
+\item 'log2': log2 transformation can be used for reducing the skewness of
 the data.
 \deqn{log2 = \log_{2} x}{%
 log2 = log2(x)}
-where \eqn{x} is a single value of data.}
+where \eqn{x} is a single value of data.
 
-\item{'normalize'}{ Make margin sum of squares equal to one. Please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'normalize': Make margin sum of squares equal to one. Please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'pa'}{ Transforms table to presence/absence table. Please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'pa': Transforms table to presence/absence table. Please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'rank'}{ Rank transformation, please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'rank': Rank transformation, please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'rclr'}{ Robust clr transformation, please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'rclr':  Robust clr transformation, please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'relabundance'}{ Relative transformation (alias for 'total'), please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'relabundance': Relative transformation (alias for 'total'), please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'rrank'}{ Relative rank transformation, please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\item 'rrank': Relative rank transformation, please refer to
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'standardize'}{ Scale 'x' to zero mean and unit variance (alias for
-'z'), please refer to \code{\link[vegan:decostand]{decostand}} for details.}
+\item 'standardize': Scale 'x' to zero mean and unit variance (alias for
+'z'), please refer to \code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'total'}{ Divide by margin total (alias for
+\item 'total': Divide by margin total (alias for
 'relabundance'), please refer to
-\code{\link[vegan:decostand]{decostand}} for details.}
+\code{\link[vegan:decostand]{decostand}} for details.
 
-\item{'z'}{ Z transformation (alias for 'standardize'),
-please refer to \code{\link[vegan:decostand]{decostand}} for details.}
+\item 'z': Z transformation (alias for 'standardize'),
+please refer to \code{\link[vegan:decostand]{decostand}} for details.
 
 }
 }