diff --git a/DESCRIPTION b/DESCRIPTION
index b774d6c..c4b7bc9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -28,7 +28,8 @@ Imports:
     sva,
     GSEABase,
     xCell,
-    MCPcounter
+    MCPcounter,
+    utils
 Suggests:
     testthat,
     knitr,
@@ -47,4 +48,4 @@ Roxygen: list(markdown = TRUE)
 LazyData: true
 URL: https://icbi-lab.github.io/immunedeconv, https://github.com/icbi-lab/immunedeconv
 BugReports: https://github.com/icbi-lab/immunedeconv/issues
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
diff --git a/NAMESPACE b/NAMESPACE
index 7a0ab12..267b3e2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(available_datasets)
+export(cell_type_map)
+export(cell_type_tree)
 export(deconvolute)
 export(deconvolute_cibersort)
 export(deconvolute_epic)
@@ -35,3 +38,4 @@ importFrom(stats,na.omit)
 importFrom(testit,assert)
 importFrom(tibble,as_tibble)
 importFrom(tibble,rowid_to_column)
+importFrom(utils,assignInMyNamespace)
diff --git a/R/cell_type_mapping.R b/R/cell_type_mapping.R
index 5d2a8c4..ca87604 100644
--- a/R/cell_type_mapping.R
+++ b/R/cell_type_mapping.R
@@ -6,19 +6,18 @@
 #' @importFrom dplyr select
 #' @importFrom stats na.omit
 #' @import magrittr
-#'
+#' 
 #' @name cell_type_mapping
 NULL
 
-
 #' Table mapping the cell types from methods/datasets to a single, controlled vocabulary.
 #'
 #' Columns: `method_dataset`, `method_cell_type`, `cell_type`.
 #'
 #' See `inst/extdata/cell_type_mapping.xlsx` for more details.
 #'
-#' @name cell_type_map
-NULL
+#' @export
+cell_type_map = NULL
 # gets attached on .onLoad, see zzz.R
 .get_cell_type_map = function() {
   readxl::read_xlsx(system.file("extdata", "cell_type_mapping.xlsx",
@@ -34,14 +33,16 @@ NULL
 #' A list of all methods (e.g. `cibersort`) and datasets (e.g. `schelker_ovarian`) for
 #' that the cell types are mapped to the controlled vocabulary.
 #'
-#' @name available_datasets
-NULL
+#' @export
+available_datasets = NULL
 # gets attached on .onLoad, see zzz.R
 .get_available_datasets = function() {
   cell_type_map %>% pull(method_dataset) %>% unique()
 }
 
 
+#' List with controlled cell-type vocabulary
+cell_type_list = NULL
 .get_cell_type_list = function() {
   tmp_list = readxl::read_excel(system.file("extdata", "cell_type_mapping.xlsx",
                                             package="immunedeconv", mustWork=TRUE),
@@ -57,14 +58,19 @@ NULL
 #'
 #' @details a `data.tree` object
 #' @name cell_type_tree
-NULL
+#' @export
+cell_type_tree = NULL
 # gets attached on .onLoad, see zzz.R
 .get_cell_type_tree = function() {
   cell_type_list %>% as.data.frame() %>% data.tree::FromDataFrameNetwork()
 }
 
 
-# Access nodes by name in O(1). Node names are unique in our tree.
+#' Lookup dictionary for cell-type nodes
+#' 
+#' Access nodes by name in O(1). Node names are unique in our tree.
+#' gets attached on .onLoad, see zzz.R
+node_by_name=NULL
 # gets attached on .onLoad, see zzz.R
 .get_node_by_name = function() {
   cell_type_tree$Get(function(node){node})
diff --git a/R/immune_deconvolution_methods.R b/R/immune_deconvolution_methods.R
index b74a78b..a4a6a68 100644
--- a/R/immune_deconvolution_methods.R
+++ b/R/immune_deconvolution_methods.R
@@ -1,5 +1,7 @@
 #' Collection of immune cell deconvolution methods.
-#'
+#' 
+#' @description Immunedeconv is an an R package for unified access to computational methods for
+#'  estimating immune cell fractions from bulk RNA sequencing data. 
 #' @docType package
 #' @name immunedeconv
 #' @import methods
diff --git a/R/zzz.R b/R/zzz.R
index 1528136..6393419 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,14 +1,17 @@
-# assign the following global variables
-# .onLoad because of 'staged-install'
-#
-# See https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
-# for more details.
-#
+#' assign the following global variables
+#' .onLoad because of 'staged-install'
+#'
+#' See https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
+#' for more details.
+#' 
+#' @name fix_namespace
+#' @importFrom utils assignInMyNamespace
+NULL
 
 .onLoad = function(libname, pkgname) {
-  assign('cell_type_map', .get_cell_type_map(), envir=.GlobalEnv)
-  assign('available_datasets', .get_available_datasets(), envir=.GlobalEnv)
-  assign('cell_type_list', .get_cell_type_list(), envir=.GlobalEnv)
-  assign('cell_type_tree', .get_cell_type_tree(), envir=.GlobalEnv)
-  assign('node_by_name', .get_node_by_name(), envir=.GlobalEnv)
+  assignInMyNamespace('cell_type_map', .get_cell_type_map())
+  assignInMyNamespace('available_datasets', .get_available_datasets())
+  assignInMyNamespace('cell_type_list', .get_cell_type_list())
+  assignInMyNamespace('cell_type_tree', .get_cell_type_tree())
+  assignInMyNamespace('node_by_name', .get_node_by_name())
 }
diff --git a/man/available_datasets.Rd b/man/available_datasets.Rd
index 705125e..ec0ce03 100644
--- a/man/available_datasets.Rd
+++ b/man/available_datasets.Rd
@@ -1,9 +1,17 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/cell_type_mapping.R
+\docType{data}
 \name{available_datasets}
 \alias{available_datasets}
 \title{Available methods and datasets.}
+\format{
+An object of class \code{character} of length 13.
+}
+\usage{
+available_datasets
+}
 \description{
 A list of all methods (e.g. \code{cibersort}) and datasets (e.g. \code{schelker_ovarian}) for
 that the cell types are mapped to the controlled vocabulary.
 }
+\keyword{datasets}
diff --git a/man/cell_type_list.Rd b/man/cell_type_list.Rd
new file mode 100644
index 0000000..a359328
--- /dev/null
+++ b/man/cell_type_list.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cell_type_mapping.R
+\docType{data}
+\name{cell_type_list}
+\alias{cell_type_list}
+\title{List with controlled cell-type vocabulary}
+\format{
+An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 65 rows and 3 columns.
+}
+\usage{
+cell_type_list
+}
+\description{
+List with controlled cell-type vocabulary
+}
+\keyword{datasets}
diff --git a/man/cell_type_map.Rd b/man/cell_type_map.Rd
index e3e02e9..100be6d 100644
--- a/man/cell_type_map.Rd
+++ b/man/cell_type_map.Rd
@@ -1,11 +1,19 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/cell_type_mapping.R
+\docType{data}
 \name{cell_type_map}
 \alias{cell_type_map}
 \title{Table mapping the cell types from methods/datasets to a single, controlled vocabulary.}
+\format{
+An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 159 rows and 3 columns.
+}
+\usage{
+cell_type_map
+}
 \description{
 Columns: \code{method_dataset}, \code{method_cell_type}, \code{cell_type}.
 }
 \details{
 See \code{inst/extdata/cell_type_mapping.xlsx} for more details.
 }
+\keyword{datasets}
diff --git a/man/cell_type_tree.Rd b/man/cell_type_tree.Rd
index 9507c04..221cbc1 100644
--- a/man/cell_type_tree.Rd
+++ b/man/cell_type_tree.Rd
@@ -1,11 +1,19 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/cell_type_mapping.R
+\docType{data}
 \name{cell_type_tree}
 \alias{cell_type_tree}
 \title{Available cell types in the controlled vocabulary organized as a lineage tree.}
+\format{
+An object of class \code{Node} (inherits from \code{R6}) of length 41.
+}
+\usage{
+cell_type_tree
+}
 \description{
 Available cell types in the controlled vocabulary organized as a lineage tree.
 }
 \details{
 a \code{data.tree} object
 }
+\keyword{datasets}
diff --git a/man/dataset_racle.Rd b/man/dataset_racle.Rd
index b8eed15..545b3f0 100644
--- a/man/dataset_racle.Rd
+++ b/man/dataset_racle.Rd
@@ -4,9 +4,11 @@
 \name{dataset_racle}
 \alias{dataset_racle}
 \title{Example RNA-seq dataset from the EPIC publication.}
-\format{an environment with two objects:
+\format{
+an environment with two objects:
 (1) \code{expr_mat}: gene expression matrix with gene_symbols as rownames and sample identifiers as colnames.
-(2) \code{ref}: FACS measurements in a data.frame with three columns: sample, cell_type, true_fraction}
+(2) \code{ref}: FACS measurements in a data.frame with three columns: sample, cell_type, true_fraction
+}
 \source{
 Racle et al. (2017), eLIFE, https://doi.org/10.7554/eLife.26476.029
 }
diff --git a/man/deconvolute.Rd b/man/deconvolute.Rd
index 6982120..b6b7b32 100644
--- a/man/deconvolute.Rd
+++ b/man/deconvolute.Rd
@@ -4,10 +4,18 @@
 \alias{deconvolute}
 \title{Perform an immune cell deconvolution on a dataset.}
 \usage{
-deconvolute(gene_expression, method = deconvolution_methods,
-  indications = NULL, tumor = TRUE, arrays = FALSE,
-  column = "gene_symbol", rmgenes = NULL, scale_mrna = TRUE,
-  expected_cell_types = NULL, ...)
+deconvolute(
+  gene_expression,
+  method = deconvolution_methods,
+  indications = NULL,
+  tumor = TRUE,
+  arrays = FALSE,
+  column = "gene_symbol",
+  rmgenes = NULL,
+  scale_mrna = TRUE,
+  expected_cell_types = NULL,
+  ...
+)
 }
 \arguments{
 \item{gene_expression}{A gene expression matrix or a Biobase ExpressionSet.
diff --git a/man/deconvolute_cibersort.Rd b/man/deconvolute_cibersort.Rd
index c0d3d52..ba51169 100644
--- a/man/deconvolute_cibersort.Rd
+++ b/man/deconvolute_cibersort.Rd
@@ -4,8 +4,13 @@
 \alias{deconvolute_cibersort}
 \title{Deconvolute using CIBERSORT or CIBERSORT abs.}
 \usage{
-deconvolute_cibersort(gene_expression_matrix, arrays, absolute = FALSE,
-  abs_method = "sig.score", ...)
+deconvolute_cibersort(
+  gene_expression_matrix,
+  arrays,
+  absolute = FALSE,
+  abs_method = "sig.score",
+  ...
+)
 }
 \arguments{
 \item{gene_expression_matrix}{a m x n matrix with m genes and n samples}
diff --git a/man/deconvolute_mcp_counter.Rd b/man/deconvolute_mcp_counter.Rd
index 212d489..8ecda2b 100644
--- a/man/deconvolute_mcp_counter.Rd
+++ b/man/deconvolute_mcp_counter.Rd
@@ -4,14 +4,17 @@
 \alias{deconvolute_mcp_counter}
 \title{Deconvolute using MCP-counter}
 \usage{
-deconvolute_mcp_counter(gene_expression_matrix,
-  feature_types = "HUGO_symbols", ...)
+deconvolute_mcp_counter(
+  gene_expression_matrix,
+  feature_types = "HUGO_symbols",
+  ...
+)
 }
 \arguments{
 \item{gene_expression_matrix}{a m x n matrix with m genes and n samples}
 
 \item{feature_types}{type of identifiers used for expression features. May be
-one of \code{"affy133P2_probesets","HUGO_symbols","ENTREZ_ID"}}
+one of \verb{"affy133P2_probesets","HUGO_symbols","ENTREZ_ID"}}
 
 \item{...}{pased through to original MCP-counter function. A native argument takes precedence
 over an immunedeconv argument (e.g. \code{featureType} takes precedence over \code{feature_types})
diff --git a/man/deconvolute_quantiseq.Rd b/man/deconvolute_quantiseq.Rd
index e08d530..f0a9136 100644
--- a/man/deconvolute_quantiseq.Rd
+++ b/man/deconvolute_quantiseq.Rd
@@ -4,8 +4,7 @@
 \alias{deconvolute_quantiseq}
 \title{Deconvolute using quanTIseq}
 \usage{
-deconvolute_quantiseq(gene_expression_matrix, tumor, arrays, scale_mrna,
-  ...)
+deconvolute_quantiseq(gene_expression_matrix, tumor, arrays, scale_mrna, ...)
 }
 \arguments{
 \item{gene_expression_matrix}{a m x n matrix with m genes and n samples}
diff --git a/man/deconvolute_quantiseq.default.Rd b/man/deconvolute_quantiseq.default.Rd
index ed1b6d8..77f88ed 100644
--- a/man/deconvolute_quantiseq.default.Rd
+++ b/man/deconvolute_quantiseq.default.Rd
@@ -4,9 +4,16 @@
 \alias{deconvolute_quantiseq.default}
 \title{Use quanTIseq to deconvolute a gene expression matrix.}
 \usage{
-deconvolute_quantiseq.default(mix.mat, arrays = FALSE,
-  signame = "TIL10", tumor = FALSE, mRNAscale = TRUE,
-  method = "lsei", btotalcells = FALSE, rmgenes = "unassigned")
+deconvolute_quantiseq.default(
+  mix.mat,
+  arrays = FALSE,
+  signame = "TIL10",
+  tumor = FALSE,
+  mRNAscale = TRUE,
+  method = "lsei",
+  btotalcells = FALSE,
+  rmgenes = "unassigned"
+)
 }
 \arguments{
 \item{mix.mat}{table with the gene TPM (or microarray expression values) for all samples to be deconvoluted
diff --git a/man/deconvolute_xcell.Rd b/man/deconvolute_xcell.Rd
index 72bb195..08dbbaa 100644
--- a/man/deconvolute_xcell.Rd
+++ b/man/deconvolute_xcell.Rd
@@ -4,8 +4,12 @@
 \alias{deconvolute_xcell}
 \title{Deconvolute using xCell}
 \usage{
-deconvolute_xcell(gene_expression_matrix, arrays,
-  expected_cell_types = NULL, ...)
+deconvolute_xcell(
+  gene_expression_matrix,
+  arrays,
+  expected_cell_types = NULL,
+  ...
+)
 }
 \arguments{
 \item{gene_expression_matrix}{a m x n matrix with m genes and n samples}
diff --git a/man/deconvolution_methods.Rd b/man/deconvolution_methods.Rd
index 873ac67..d0a7777 100644
--- a/man/deconvolution_methods.Rd
+++ b/man/deconvolution_methods.Rd
@@ -4,7 +4,9 @@
 \name{deconvolution_methods}
 \alias{deconvolution_methods}
 \title{List of supported immune deconvolution methods}
-\format{An object of class \code{character} of length 7.}
+\format{
+An object of class \code{character} of length 7.
+}
 \usage{
 deconvolution_methods
 }
diff --git a/man/fix_namespace.Rd b/man/fix_namespace.Rd
new file mode 100644
index 0000000..0c58c47
--- /dev/null
+++ b/man/fix_namespace.Rd
@@ -0,0 +1,10 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{fix_namespace}
+\alias{fix_namespace}
+\title{assign the following global variables
+.onLoad because of 'staged-install'}
+\description{
+See https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
+for more details.
+}
diff --git a/man/immunedeconv.Rd b/man/immunedeconv.Rd
index 6bc04e8..81887f8 100644
--- a/man/immunedeconv.Rd
+++ b/man/immunedeconv.Rd
@@ -3,8 +3,8 @@
 \docType{package}
 \name{immunedeconv}
 \alias{immunedeconv}
-\alias{immunedeconv-package}
 \title{Collection of immune cell deconvolution methods.}
 \description{
-Collection of immune cell deconvolution methods.
+Immunedeconv is an an R package for unified access to computational methods for
+estimating immune cell fractions from bulk RNA sequencing data.
 }
diff --git a/man/node_by_name.Rd b/man/node_by_name.Rd
new file mode 100644
index 0000000..7ee4df9
--- /dev/null
+++ b/man/node_by_name.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cell_type_mapping.R
+\docType{data}
+\name{node_by_name}
+\alias{node_by_name}
+\title{Lookup dictionary for cell-type nodes}
+\format{
+An object of class \code{list} of length 66.
+}
+\usage{
+node_by_name
+}
+\description{
+Access nodes by name in O(1). Node names are unique in our tree.
+gets attached on .onLoad, see zzz.R
+}
+\keyword{datasets}
diff --git a/man/timer_available_cancers.Rd b/man/timer_available_cancers.Rd
index 875a865..b892445 100644
--- a/man/timer_available_cancers.Rd
+++ b/man/timer_available_cancers.Rd
@@ -4,7 +4,9 @@
 \name{timer_available_cancers}
 \alias{timer_available_cancers}
 \title{TIMER signatures are cancer specific. This is the list of available cancer types.}
-\format{An object of class \code{character} of length 32.}
+\format{
+An object of class \code{character} of length 32.
+}
 \usage{
 timer_available_cancers
 }
diff --git a/man/xCell.data.Rd b/man/xCell.data.Rd
index 92406cf..ece30fc 100644
--- a/man/xCell.data.Rd
+++ b/man/xCell.data.Rd
@@ -4,7 +4,9 @@
 \name{xCell.data}
 \alias{xCell.data}
 \title{Data object from xCell.}
-\format{An object of class \code{list} of length 4.}
+\format{
+An object of class \code{list} of length 4.
+}
 \usage{
 xCell.data
 }