diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4e20ef2..85f2aeb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,10 @@
 ## SINCLAIR development version
 
 - Set main job memory to 2 GB for slurm mode. (#205, @kelly-sovacool)
+- Improvements to R Markdown reports: (#216, @kelly-sovacool)
+    - Link to function documentation websites.
+    - Use code folding to include code in output, but set it to 'hide' by default.
+    - Hide R messages by default.
 
 ## SINCLAIR 0.3.5
 
diff --git a/bin/batch_correction_cca.Rmd b/bin/batch_correction_cca.Rmd
index 93ce5fc..a21ea7f 100755
--- a/bin/batch_correction_cca.Rmd
+++ b/bin/batch_correction_cca.Rmd
@@ -1,8 +1,12 @@
 ---
 title: "Batch Correction: CCA"
-author: "Samantha Sevilla"
+author: "CCR Collaborative Bioinformatics Resource"
 date: "`r Sys.Date()`"
-output: html_document
+output:
+  html_document:
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 params:
@@ -17,9 +21,14 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
 
-
-```{r, prep_args,  message=FALSE}
+```{r, prep_args}
 # set up params
 species <- params$species
 gid <- params$gid
@@ -38,7 +47,7 @@ testing <- params$testing
 scRNA_functions <- params$scRNA_functions
 ```
 
-```{r, handle_pkg, message=FALSE}
+```{r, handle_pkg}
 # source functions
 source(scRNA_functions)
 
@@ -62,7 +71,7 @@ scRNA_handle_packages(pkg_df)
 options(future.globals.maxSize = 96000 * 1024^2)
 ```
 
-```{r, processing, message=FALSE}
+```{r, processing}
 # read in merged object
 so <- readRDS(mergedObj)
 
@@ -78,7 +87,7 @@ so_corrected <- MAIN_BATCH_CORRECTION(so, npcs, species, resolution,
 )
 ```
 
-```{r saveoutputs, message=FALSE, include=FALSE, echo=FALSE}
+```{r saveoutputs include=FALSE}
 fpath <- paste0(gid, "_batch_correction_cca.rds")
 saveRDS(so_corrected, fpath)
 ```
diff --git a/bin/batch_correction_harmony.Rmd b/bin/batch_correction_harmony.Rmd
index e2b8753..215efba 100755
--- a/bin/batch_correction_harmony.Rmd
+++ b/bin/batch_correction_harmony.Rmd
@@ -1,8 +1,12 @@
 ---
 title: "Batch Correction: Harmony"
-author: "Samantha Sevilla"
+author: "CCR Collaborative Bioinformatics Resource"
 date: "`r Sys.Date()`"
-output: html_document
+output:
+  html_document:
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 params:
@@ -17,8 +21,13 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
-
-```{r, prep_args,  message=FALSE, echo=FALSE, include=FALSE}
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
+```{r, prep_args, include=FALSE}
 # set up params
 species <- params$species
 gid <- params$gid
@@ -36,7 +45,7 @@ Rpkg_config <- params$Rpkg_config
 scRNA_functions <- params$scRNA_functions
 ```
 
-```{r, handle_pkg, message=FALSE}
+```{r, handle_pkg}
 # source functions
 source(scRNA_functions)
 
@@ -60,7 +69,7 @@ scRNA_handle_packages(pkg_df)
 options(future.globals.maxSize = 96000 * 1024^2)
 ```
 
-```{r, processing, message=FALSE}
+```{r, processing}
 # read in merged object
 so <- readRDS(mergedObj)
 
@@ -76,7 +85,7 @@ so_corrected <- MAIN_BATCH_CORRECTION(so, npcs, species, resolution,
 )
 ```
 
-```{r saveoutputs, message=FALSE, include=FALSE, echo=FALSE}
+```{r saveoutputs include=FALSE}
 fpath <- paste0(gid, "_batch_correction_harmony.rds")
 saveRDS(so_corrected, fpath)
 ```
diff --git a/bin/batch_correction_integration.Rmd b/bin/batch_correction_integration.Rmd
index d96a7ad..7b0f6d7 100755
--- a/bin/batch_correction_integration.Rmd
+++ b/bin/batch_correction_integration.Rmd
@@ -1,8 +1,12 @@
 ---
 title: "Batch Correction Analysis"
-author: "CCBR"
-date: '`r format(Sys.time(), "%a %b %d %Y - %X")`'
-output: html_document
+author: "CCR Collaborative Bioinformatics Resource"
+date: "`r Sys.Date()`"
+output:
+  html_document:
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 always_allow_html: true
@@ -23,8 +27,13 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
-
-```{r, prep_args,  message=FALSE, echo=FALSE, include=FALSE}
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
+```{r, prep_args, include=FALSE}
 # set up params
 # species= params$species
 gid <- params$gid
@@ -51,7 +60,7 @@ unlink(tmp_images, recursive = TRUE)
 dir.create(file.path("tmp_images"), showWarnings = FALSE)
 ```
 
-```{r, handle_pkg, message=FALSE, echo=FALSE, include=FALSE}
+```{r, handle_pkg  include=FALSE}
 # source functions
 source(scRNA_functions)
 
@@ -71,7 +80,7 @@ pkg_df
 scRNA_handle_packages(pkg_df)
 ```
 
-```{r, processing, message=FALSE, echo=FALSE, include=FALSE}
+```{r, processing  include=FALSE}
 # read in merged objects
 so_merged <- readRDS(mergedObj)
 so_rpca <- readRDS(rpcaObj)
@@ -89,7 +98,7 @@ objList <- c("merged", "rpca", "integrated", "harmony", "liger")
 
 ### Samples
 
-```{r sampleBatchCorrection, echo=FALSE, fig.width=15, fig.height=15}
+```{r sampleBatchCorrection, fig.width=15, fig.height=15}
 # plot
 plot_list_s <- list()
 
@@ -123,7 +132,7 @@ annotate_figure(p,
 
 ### Groups
 
-```{r groupBatchCorrection, echo=FALSE, fig.width=15, fig.height=15}
+```{r groupBatchCorrection, fig.width=15, fig.height=15}
 plot_list_g <- list()
 for (i in 1:length(objList)) {
   obj <- OBJECT_SELECT(objList[i])
@@ -150,7 +159,7 @@ annotate_figure(p,
 
 ### Cell type annotations
 
-```{r annotationBatchCorrection, echo=FALSE, fig.width=15, fig.height=15}
+```{r annotationBatchCorrection, fig.width=15, fig.height=15}
 plot_list_annot <- list()
 for (i in 1:length(objList)) {
   obj <- OBJECT_SELECT(objList[i])
@@ -187,7 +196,7 @@ DT::datatable(
 
 ### RPCA
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "rpca"
 files <- list.files(
   path = tmp_images,
@@ -203,7 +212,7 @@ if (length(files) > 0) {
 
 ### ccaIntegrated
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "int"
 files <- list.files(
   path = tmp_images,
@@ -219,7 +228,7 @@ if (length(files) > 0) {
 
 ### Harmony
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "harmony"
 files <- list.files(
   path = tmp_images,
@@ -237,7 +246,7 @@ if (length(files) > 0) {
 
 ### scvi
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "scvi"
 files <- list.files(
   path = tmp_images,
@@ -255,7 +264,7 @@ if (length(files) > 0) {
 
 ### liger
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "liger"
 files <- list.files(
   path = tmp_images,
@@ -271,7 +280,7 @@ if (length(files) > 0) {
 
 ## Silhouette scores  {.tabset}
 
-```{r silhouetteImages,   message=FALSE, echo=FALSE, include=FALSE}
+```{r silhouetteImages,   , include=FALSE}
 # create matrix
 resSil_merged <- matrix(ncol = 2, nrow = length(resolution))
 resSil_merged[] <- 0
@@ -412,7 +421,7 @@ for (i in 1:length(objList)) {
 
 ### RPCA
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "rpca"
 files <- list.files(
   path = tmp_images,
@@ -428,7 +437,7 @@ if (length(files) > 0) {
 
 ### ccaIntegrated
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "int"
 files <- list.files(
   path = tmp_images,
@@ -444,7 +453,7 @@ if (length(files) > 0) {
 
 ### Harmony
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "harmony"
 files <- list.files(
   path = tmp_images,
@@ -462,7 +471,7 @@ if (length(files) > 0) {
 
 ### scvi
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "scvi"
 files <- list.files(
   path = tmp_images,
@@ -480,7 +489,7 @@ if (length(files) > 0) {
 
 ### liger
 
-```{r, echo=FALSE,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
+```{r,out.width="49%", out.height="20%",fig.show='hold',fig.align='center'}
 method <- "liger"
 files <- list.files(
   path = tmp_images,
diff --git a/bin/batch_correction_liger.Rmd b/bin/batch_correction_liger.Rmd
index 7df5d5d..efb1ff8 100755
--- a/bin/batch_correction_liger.Rmd
+++ b/bin/batch_correction_liger.Rmd
@@ -1,8 +1,12 @@
 ---
 title: 'Batch Correction: LIGER'
-author: "Samantha Sevilla"
+author: "CCR Collaborative Bioinformatics Resource"
 date: "`r Sys.Date()`"
-output: html_document
+output:
+  html_document:
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 params:
@@ -17,9 +21,14 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
 
-
-```{r, prep_args,  message=FALSE}
+```{r, prep_args}
 # set up params
 species <- params$species
 gid <- params$gid
@@ -38,7 +47,7 @@ testing <- params$testing
 scRNA_functions <- params$scRNA_functions
 ```
 
-```{r, handle_pkg, message=FALSE}
+```{r, handle_pkg}
 # source functions
 source(scRNA_functions)
 
@@ -62,7 +71,7 @@ scRNA_handle_packages(pkg_df)
 options(future.globals.maxSize = 96000 * 1024^2)
 ```
 
-```{r, processing, message=FALSE}
+```{r, processing}
 # read in merged object
 so <- readRDS(mergedObj)
 
@@ -78,7 +87,7 @@ so_corrected <- MAIN_BATCH_CORRECTION(so, npcs, species, resolution,
 )
 ```
 
-```{r saveoutputs, message=FALSE, include=FALSE, echo=FALSE}
+```{r saveoutputs include=FALSE}
 fpath <- paste0(gid, "_batch_correction_liger.rds")
 saveRDS(so_corrected, fpath)
 ```
diff --git a/bin/batch_correction_rpca.Rmd b/bin/batch_correction_rpca.Rmd
index 7d15127..89b9503 100755
--- a/bin/batch_correction_rpca.Rmd
+++ b/bin/batch_correction_rpca.Rmd
@@ -1,8 +1,12 @@
 ---
 title: "Batch Correction: rpca"
-author: "Samantha Sevilla"
+author: "CCR Collaborative Bioinformatics Resource"
 date: "`r Sys.Date()`"
-output: html_document
+output:
+  html_document:
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 params:
@@ -17,8 +21,13 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
-
-```{r, prep_args,  message=FALSE, echo=FALSE, include=FALSE}
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
+```{r, prep_args, include=FALSE}
 # set up params
 species <- params$species
 gid <- params$gid
@@ -36,7 +45,7 @@ Rpkg_config <- params$Rpkg_config
 scRNA_functions <- params$scRNA_functions
 ```
 
-```{r, handle_pkg, message=FALSE}
+```{r, handle_pkg}
 # source functions
 source(scRNA_functions)
 
@@ -60,7 +69,7 @@ scRNA_handle_packages(pkg_df)
 options(future.globals.maxSize = 96000 * 1024^2)
 ```
 
-```{r, processing, message=FALSE}
+```{r, processing}
 # read in merged object
 so <- readRDS(mergedObj)
 
@@ -76,7 +85,7 @@ so_corrected <- MAIN_BATCH_CORRECTION(so, npcs, species, resolution,
 )
 ```
 
-```{r saveoutputs, message=FALSE, include=FALSE, echo=FALSE}
+```{r saveoutputs include=FALSE}
 fpath <- paste0(gid, "_batch_correction_rpca.rds")
 saveRDS(so_corrected, fpath)
 ```
diff --git a/bin/batch_correction_scvi.Rmd b/bin/batch_correction_scvi.Rmd
index d1e4a31..0f4c727 100755
--- a/bin/batch_correction_scvi.Rmd
+++ b/bin/batch_correction_scvi.Rmd
@@ -1,8 +1,12 @@
 ---
 title: "Batch Correction: scvi"
-author: "Samantha Sevilla"
+author: "CCR Collaborative Bioinformatics Resource"
 date: "`r Sys.Date()`"
-output: html_document
+output:
+  html_document:
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 params:
@@ -19,8 +23,13 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
-
-```{r, prep_args,  message=FALSE, echo=FALSE, include=FALSE}
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
+```{r, prep_args, include=FALSE}
 # set up params
 species <- params$species
 gid <- params$gid
@@ -40,7 +49,7 @@ Rpkg_config <- params$Rpkg_config
 scRNA_functions <- params$scRNA_functions
 ```
 
-```{r, handle_pkg, message=FALSE, echo=FALSE, include=FALSE}
+```{r, handle_pkg  include=FALSE}
 # source functions
 source(scRNA_functions)
 
@@ -66,7 +75,7 @@ reticulate::use_python(python_path)
 options(future.globals.maxSize = 96000 * 1024^2)
 ```
 
-```{r, processing,  message=FALSE, echo=FALSE, include=FALSE}
+```{r, processing, include=FALSE}
 # read in merged object
 so <- readRDS(mergedObj)
 
@@ -84,7 +93,7 @@ so_corrected <- MAIN_BATCH_CORRECTION(so, npcs, species, resolution,
 so_corrected
 ```
 
-```{r saveoutputs, message=FALSE, include=FALSE, echo=FALSE}
+```{r saveoutputs include=FALSE}
 fpath <- paste0(gid, "_batch_correction_scvi.rds")
 saveRDS(so_corrected, fpath)
 ```
diff --git a/bin/seurat_merge.Rmd b/bin/seurat_merge.Rmd
index 49e5212..fe06ddb 100755
--- a/bin/seurat_merge.Rmd
+++ b/bin/seurat_merge.Rmd
@@ -1,8 +1,12 @@
 ---
 title: "merge Notebook"
+author: "CCR Collaborative Bioinformatics Resource"
+date: "`r Sys.Date()`"
 output:
   html_document:
-    toc: yes
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 params:
@@ -17,8 +21,13 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "Y"
 ---
-
-```{r, prep_args,  message=FALSE, include=FALSE}
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
+```{r, prep_args, include=FALSE}
 # set up params
 species <- params$species
 vars_to_regress <- params$vars_to_regress
@@ -43,7 +52,7 @@ print(paste0("vars_to_regress_list:", vars_to_regress_list))
 print(paste0("gid:", gid))
 ```
 
-```{r, handle_pkg, message=FALSE, include=FALSE}
+```{r, handle_pkg include=FALSE}
 # set library dir, load this and remove any other dirs to avoid confusion
 # between personally created pkgs and the pipeline package
 ## saving old path "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library"
@@ -88,7 +97,7 @@ source(scRNA_functions)
 options(future.globals.maxSize = 1e12)
 ```
 
-```{r, processing, message=FALSE}
+```{r, processing}
 # print group info
 print(paste0("This merged object includes groups: ", gid))
 
@@ -117,7 +126,7 @@ for (p in readObj) { # TODO use map instead of a for loop
 }
 ```
 
-```{r merge_objs, message=FALSE}
+```{r merge_objs}
 # create ref list
 reference.list <- combinedObj.list[unlist(readObj)]
 
@@ -132,7 +141,7 @@ combinedObj.integratedRNA <- merge(reference.list[[1]], reference.list[2:length(
 VariableFeatures(combinedObj.integratedRNA) <- selectFeatures
 ```
 
-```{r mergedObjDims, message=FALSE, echo=FALSE}
+```{r mergedObjDims }
 # vars.to.regress is NULL by default
 so_merged <- SCTransform(combinedObj.integratedRNA, vars.to.regress = vars_to_regress_list, assay = "RNA")
 
diff --git a/bin/seurat_preprocess.Rmd b/bin/seurat_preprocess.Rmd
index 76fdd91..4feac39 100755
--- a/bin/seurat_preprocess.Rmd
+++ b/bin/seurat_preprocess.Rmd
@@ -1,8 +1,12 @@
 ---
 title: "scRNA Notebook"
+author: "CCR Collaborative Bioinformatics Resource"
+date: "`r Sys.Date()`"
 output:
   html_document:
-    toc: yes
+    toc: true
+    code_folding: hide
+    downlit_highlight: true
 editor_options:
   chunk_output_type: console
 params:
@@ -23,8 +27,14 @@ params:
   scRNA_functions: "/data/CCBR_Pipeliner/Pipelines/SINCLAIR/dev/bin/scRNA_functions.R"
   testing: "N"
 ---
+```{r, setup, include=FALSE}
+knitr::opts_chunk$set(
+  message = FALSE,
+  echo = TRUE
+)
+```
 
-```{r, prep_args, message=FALSE}
+```{r, prep_args}
 # set up params
 species <- params$species
 sampleid <- params$sampleid
@@ -47,7 +57,7 @@ scRNA_functions <- params$scRNA_functions
 testing <- params$testing
 ```
 
-```{r, handle_pkg, message=FALSE}
+```{r, handle_pkg}
 # set library dir, load this and remove any other dirs to avoid confusion
 # between personally created pkgs and the pipeline package
 ## saving old path "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library"
@@ -91,7 +101,7 @@ source(scRNA_functions)
 # tinytex::install_tinytex(force = TRUE)
 ```
 
-```{r, pre-processing, message=FALSE}
+```{r, pre-processing}
 # read in h5 file
 rnaCounts <- Read10X_h5(h5)
 
@@ -116,7 +126,7 @@ FeatureScatter(so, feature1 = "nFeature_RNA", feature2 = "percent.mt")
 VlnPlot(so, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
 ```
 
-```{r, QC, message=FALSE}
+```{r, QC}
 # subset
 so_filt <- subset(so, subset = nFeature_RNA > 200)
 so_filt
@@ -132,7 +142,7 @@ so_qc <- RunMiQC(so_filt,
 # ggplot2::scale_color_gradient(low = "grey", high = "purple")
 ```
 
-```{r qc2, message=FALSE}
+```{r qc2}
 # define feature info
 nCount_out <- outliers_mad(so_qc$nCount_RNA, threshold = 3)$LL_CI_MAD
 nFeature_out <- outliers_mad(so_qc$nFeature_RNA, threshold = 3)$LL_CI_MAD
@@ -169,7 +179,7 @@ so_labeled <- MAIN_SINGLER(so_processed, species)
 so_doublet <- MAIN_DOUBLETS(so_labeled, run_doublet_finder)
 ```
 
-```{r, save, message=FALSE}
+```{r, save}
 # clean final object
 so_output <- UpdateSeuratObject(so_doublet)
 so_output