diff --git a/NAMESPACE b/NAMESPACE
index 403f46f5a..8e846645b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -40,8 +40,6 @@ export(complete_cases)
 export(compute_pooled)
 export(contrasts_fisher_exact)
 export(contrasts_linfct)
-export(copy_SAINTe_doc)
-export(copy_mixed_model_analysis_script)
 export(cor_jackknife_matrix)
 export(cor_order)
 export(create_config_MQ_peptide)
@@ -143,7 +141,6 @@ export(remove_NA_rows)
 export(remove_large_QValues)
 export(remove_small_intensities)
 export(render_MQSummary_rmd)
-export(render_SummarizeFiltering_rmd)
 export(response_as_matrix)
 export(response_matrix_as_tibble)
 export(rlm_estimate)
@@ -152,6 +149,7 @@ export(robust_scale)
 export(sample_subset)
 export(scale_with_subset)
 export(scale_with_subset_by_factors)
+export(scriptCopyHelperVec)
 export(separate_factors)
 export(separate_hierarchy)
 export(setup_analysis)
diff --git a/R/vignetteHelpers.R b/R/vignetteHelpers.R
index 86490006f..0b4bd68b3 100644
--- a/R/vignetteHelpers.R
+++ b/R/vignetteHelpers.R
@@ -1,7 +1,9 @@
 #' find file stored in package
 #' @export
+#' @keywords internal
 #' @examples
 #' find_package_file("prolfqua","extdata/medata.csv")
+#'
 find_package_file <- function(packagename, file){
 
   src_script <- file.path(find.package(packagename) , file )
@@ -17,8 +19,10 @@ find_package_file <- function(packagename, file){
 
 }
 
-
-.scriptCopyHelperVec <-
+#' copy script files and other from a package to workdir
+#' @export
+#' @keywords internal
+scriptCopyHelperVec <-
   function(runscripts,
            workdir = getwd(),
            packagename = "prolfqua") {
@@ -49,35 +53,6 @@ find_package_file <- function(packagename, file){
     return(res)
   }
 
-#' copy all files need to run mixed model analysis.
-#' @param workdir directory where to copy file - default is current working directory.
-#' @keywords internal
-#' @export
-#' @examples
-#' copy_mixed_model_analysis_script(workdir = tempdir())
-copy_mixed_model_analysis_script <- function(workdir = getwd()){
-  runscripts <- c("fgcz_formatting/fgcz_header.html",
-                  "fgcz_formatting/fgcz_footer.html",
-                  "fgcz_formatting/fgcz.css",
-                  "fgcz_formatting/fgcz_banner.png",
-                  "rmarkdown/mixed_model_analysis_script_Report.Rmd",
-                  "rmarkdown/bibliography.bib"
-                  )
-  .scriptCopyHelperVec(runscripts, workdir = workdir)
-}
-
-
-
-#' copy SAINTexpress doc file
-#' @param workdir directory where to copy file - default is current working directory.
-#' @keywords internal
-#' @export
-#' @examples
-#' copy_SAINTe_doc(workdir = tempdir())
-copy_SAINTe_doc <- function(workdir = getwd()){
-  runscripts <- c("SaintExpress/SAINTexpress-manual.docx")
-  .scriptCopyHelperVec(runscripts, workdir = workdir)
-}
 
 .run_markdown_with_params <-
   function(params,
@@ -87,7 +62,7 @@ copy_SAINTe_doc <- function(workdir = getwd()){
            workdir = tempdir(),
            packagename = "prolfqua",
            format = "pdf") {
-    res <- .scriptCopyHelperVec(markdown_path,
+    res <- prolfqua::scriptCopyHelperVec(markdown_path,
                                 workdir = workdir,
                                 packagename = packagename)
     dist_file_path <-
@@ -168,27 +143,3 @@ render_MQSummary_rmd <-
 
 
 
-#' render Filtering Summary.
-#' @param pdata data.frame
-#' @param config AnalysisConfiguration
-#'
-#' @family vignetteHelpers
-#' @keywords internal
-#'
-#' @export
-#'
-render_SummarizeFiltering_rmd <-
-  function(results,
-           dest_path = ".",
-           dest_file_name = "Summarize_Filtering.pdf",
-           workdir = tempdir())
-  {
-    dist_file_path <- .run_markdown_with_params(
-      results,
-      markdown_path = "rmarkdown/Summarize_Filtering.Rmd",
-      dest_path = dest_path,
-      dest_file_name = dest_file_name,
-      workdir = workdir,
-      packagename = "prolfqua"
-    )
-  }
diff --git a/man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd b/man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd
index 5e00152c9..5f46a4d72 100644
--- a/man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd
+++ b/man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd
@@ -150,8 +150,7 @@ Other utilities:
 \code{\link{table_facade}()}
 
 Other vignetteHelpers: 
-\code{\link{render_MQSummary_rmd}()},
-\code{\link{render_SummarizeFiltering_rmd}()}
+\code{\link{render_MQSummary_rmd}()}
 }
 \concept{FragPipe}
 \concept{MaxQuant}
diff --git a/man/copy_SAINTe_doc.Rd b/man/copy_SAINTe_doc.Rd
deleted file mode 100644
index 2c6ebc56e..000000000
--- a/man/copy_SAINTe_doc.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/vignetteHelpers.R
-\name{copy_SAINTe_doc}
-\alias{copy_SAINTe_doc}
-\title{copy SAINTexpress doc file}
-\usage{
-copy_SAINTe_doc(workdir = getwd())
-}
-\arguments{
-\item{workdir}{directory where to copy file - default is current working directory.}
-}
-\description{
-copy SAINTexpress doc file
-}
-\examples{
-copy_SAINTe_doc(workdir = tempdir())
-}
-\keyword{internal}
diff --git a/man/copy_mixed_model_analysis_script.Rd b/man/copy_mixed_model_analysis_script.Rd
deleted file mode 100644
index d337d4494..000000000
--- a/man/copy_mixed_model_analysis_script.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/vignetteHelpers.R
-\name{copy_mixed_model_analysis_script}
-\alias{copy_mixed_model_analysis_script}
-\title{copy all files need to run mixed model analysis.}
-\usage{
-copy_mixed_model_analysis_script(workdir = getwd())
-}
-\arguments{
-\item{workdir}{directory where to copy file - default is current working directory.}
-}
-\description{
-copy all files need to run mixed model analysis.
-}
-\examples{
-copy_mixed_model_analysis_script(workdir = tempdir())
-}
-\keyword{internal}
diff --git a/man/find_package_file.Rd b/man/find_package_file.Rd
index a3f0aaaf8..758ba123e 100644
--- a/man/find_package_file.Rd
+++ b/man/find_package_file.Rd
@@ -11,4 +11,6 @@ find file stored in package
 }
 \examples{
 find_package_file("prolfqua","extdata/medata.csv")
+
 }
+\keyword{internal}
diff --git a/man/render_MQSummary_rmd.Rd b/man/render_MQSummary_rmd.Rd
index 135b3b4f4..b5ce591d5 100644
--- a/man/render_MQSummary_rmd.Rd
+++ b/man/render_MQSummary_rmd.Rd
@@ -50,8 +50,7 @@ render_MQSummary_rmd(analysis,
 }
 \seealso{
 Other vignetteHelpers: 
-\code{\link{INTERNAL_FUNCTIONS_BY_FAMILY}},
-\code{\link{render_SummarizeFiltering_rmd}()}
+\code{\link{INTERNAL_FUNCTIONS_BY_FAMILY}}
 }
 \concept{vignetteHelpers}
 \keyword{internal}
diff --git a/man/render_SummarizeFiltering_rmd.Rd b/man/render_SummarizeFiltering_rmd.Rd
deleted file mode 100644
index 79a86852a..000000000
--- a/man/render_SummarizeFiltering_rmd.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/vignetteHelpers.R
-\name{render_SummarizeFiltering_rmd}
-\alias{render_SummarizeFiltering_rmd}
-\title{render Filtering Summary.}
-\usage{
-render_SummarizeFiltering_rmd(
-  results,
-  dest_path = ".",
-  dest_file_name = "Summarize_Filtering.pdf",
-  workdir = tempdir()
-)
-}
-\arguments{
-\item{pdata}{data.frame}
-
-\item{config}{AnalysisConfiguration}
-}
-\description{
-render Filtering Summary.
-}
-\seealso{
-Other vignetteHelpers: 
-\code{\link{INTERNAL_FUNCTIONS_BY_FAMILY}},
-\code{\link{render_MQSummary_rmd}()}
-}
-\concept{vignetteHelpers}
-\keyword{internal}
diff --git a/man/scriptCopyHelperVec.Rd b/man/scriptCopyHelperVec.Rd
new file mode 100644
index 000000000..6c865c5ed
--- /dev/null
+++ b/man/scriptCopyHelperVec.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vignetteHelpers.R
+\name{scriptCopyHelperVec}
+\alias{scriptCopyHelperVec}
+\title{copy script files and other from a package to workdir}
+\usage{
+scriptCopyHelperVec(runscripts, workdir = getwd(), packagename = "prolfqua")
+}
+\description{
+copy script files and other from a package to workdir
+}
+\keyword{internal}
diff --git a/vignettes/QualityControlAndSampleSizeEstimation.Rmd b/vignettes/QualityControlAndSampleSizeEstimation.Rmd
index 38eb16098..02c10a92d 100644
--- a/vignettes/QualityControlAndSampleSizeEstimation.Rmd
+++ b/vignettes/QualityControlAndSampleSizeEstimation.Rmd
@@ -33,9 +33,7 @@ Generate Simulated data. To learn how to create prolfqua LFQData objects see the
 ```{r filterdata}
 simdata <- prolfqua::sim_lfq_data_peptide_config()
 lfqdata <- prolfqua::LFQData$new(simdata$data,simdata$config)
-
 lfqdata$remove_small_intensities()
-
 ```
 
 You can convert the data into a data frame in a wide format, where the