diff --git a/NAMESPACE b/NAMESPACE
index 1414b29..a64504f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,6 +4,7 @@ export(BMplotPCA)
 export(DESeq2_module)
 export(biomaRt_anno_orth)
 export(brucemoran_rnaseq_kallisto_parser)
+export(dupradar_run)
 export(edgeR_module)
 export(fgsea_plot)
 export(fgsea_ssgsea_msviper)
@@ -20,6 +21,7 @@ export(make_aracne_inputs)
 export(master_parse_join)
 export(msigdb_pathways_to_list)
 export(nf_core_rnaseq_featco_parser)
+export(nf_core_rnaseq_star_salmon_parser)
 export(obs_raw_widen)
 export(parse_aracne)
 export(per_contrast_fgsea_de)
diff --git a/R/dupradar.R b/R/dupradar.R
index 2c43c33..017fce1 100644
--- a/R/dupradar.R
+++ b/R/dupradar.R
@@ -18,17 +18,18 @@ dupradar_run <- function(gtf, paired, stranded = '0', threads) {
 
   for (x in 1:length(in_bams)){
 
-  dup_out <- lapply(seq_along(in_bams), function(x){
-    dupo <- dupRadar::analyzeDuprates(in_bams[x], gtf, stranded, paired, threads)
-    pdf(paste0("dupradar/", in_bams[[x]], ".duprate_exp_densplot.pdf"))
-      dupRadar::duprateExpDensPlot(DupMat = dupo)
-    dev.off()
+    dup_out <- lapply(seq_along(in_bams), function(x){
+      dupo <- dupRadar::analyzeDuprates(in_bams[x], gtf, stranded, paired, threads)
+      pdf(paste0("dupradar/", in_bams[[x]], ".duprate_exp_densplot.pdf"))
+        dupRadar::duprateExpDensPlot(DupMat = dupo)
+      dev.off()
 
-    pdf(paste0("dupradar/", in_bams[[x]], ".duprate_exp_boxplot.pdf"))
-      dupRadar::duprateExpBoxplot(DupMat = dupo)
-    dev.off()
-    return(dupo)
-  })
-  names(dup_out) <- in_bams
-  save(dup_out, file="dupradar/dupradar.analyzeDuprates.RData")
+      pdf(paste0("dupradar/", in_bams[[x]], ".duprate_exp_boxplot.pdf"))
+        dupRadar::duprateExpBoxplot(DupMat = dupo)
+      dev.off()
+      return(dupo)
+    })
+    names(dup_out) <- in_bams
+    save(dup_out, file="dupradar/dupradar.analyzeDuprates.RData")
+  }
 }
diff --git a/R/wrapper_scripts.R b/R/wrapper_scripts.R
index 766e5b5..51cceb2 100644
--- a/R/wrapper_scripts.R
+++ b/R/wrapper_scripts.R
@@ -140,7 +140,7 @@ run_prep_modules_bm <- function(metadata_csv, metadata_design, tag, output_dir =
        file = paste0(outdir, "/", tag, ".full_results.RData"))
 
   ##per contrast DE overlap with pathways, and gene sets in lists
-  pc_fgsea_limma_de_list <- per_contrast_fgsea_de(fgsea_list_limma_rank_fithree, occupancy = 5)
+  pc_fgsea_limma_de_list <- RNAseqon::per_contrast_fgsea_de(fgsea_list_limma_rank_fithree, occupancy = 5)
   names(pc_fgsea_limma_de_list) <- names(fgsea_list_limma_rank_fithree)
 
   ##use these as input to ssGSEA in GSVA
@@ -157,7 +157,7 @@ run_prep_modules_bm <- function(metadata_csv, metadata_design, tag, output_dir =
   metadata_pca <- dplyr::select(.data = metadata_tb, sample, !!metadata_cov)
 
   pc_ssgsea_list <- lapply(names(pc_fgsea_limma_de_list), function(f){
-                      ssgsea_pca_list <- ssgsea_pca(pways = pc_fgsea_limma_de_list[[f]][[2]],
+                      ssgsea_pca_list <- RNAseqon::ssgsea_pca(pways = pc_fgsea_limma_de_list[[f]][[2]],
                                                     log2tpm_mat = agg_log2tpm_ext_mat,
                                                     msigdb_cat = "H",
                                                     output_dir = output_dir,
@@ -169,5 +169,5 @@ run_prep_modules_bm <- function(metadata_csv, metadata_design, tag, output_dir =
   ##aracne inputs
   design_vec <- unlist(lapply(metadata_design, function(f){gsub(" ", "", strsplit(f, "\\+")[[1]])}))
   CONDITION <- rev(design_vec)[1]
-  make_aracne_inputs(tpm_tb, metadata = metadata_tb, meta_group = CONDITION, tag = tag)
+  RNAseqon::make_aracne_inputs(tpm_tb, metadata = metadata_tb, meta_group = CONDITION, tag = tag)
 }
diff --git a/man/dupradar_run.Rd b/man/dupradar_run.Rd
new file mode 100644
index 0000000..aeccaa1
--- /dev/null
+++ b/man/dupradar_run.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dupradar.R
+\name{dupradar_run}
+\alias{dupradar_run}
+\title{Function to run fGSEA using the mSIGDB database from Broad}
+\usage{
+dupradar_run(gtf, paired, stranded = "0", threads)
+}
+\arguments{
+\item{gtf}{path/to/GTF.gtf}
+
+\item{paired}{boolean of whether BAM data is paired}
+
+\item{stranded}{string '0', '1', '2', indicating 'unstranded', 'forward', reverse' respectively}
+
+\item{threads}{total threads used to run}
+}
+\value{
+RData object of dupRadar outputs in list
+}
+\description{
+Function to run fGSEA using the mSIGDB database from Broad
+}
diff --git a/man/nf_core_rnaseq_star_salmon_parser.Rd b/man/nf_core_rnaseq_star_salmon_parser.Rd
new file mode 100644
index 0000000..aaf4c53
--- /dev/null
+++ b/man/nf_core_rnaseq_star_salmon_parser.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prep_RNAseq_output.R
+\name{nf_core_rnaseq_star_salmon_parser}
+\alias{nf_core_rnaseq_star_salmon_parser}
+\title{Parse featurecounts input as a follow-on from standard nf-core/rnaseq pipeline using STAR-Salmon (v3.3 currently)}
+\usage{
+nf_core_rnaseq_star_salmon_parser(tag = NULL)
+}
+\arguments{
+\item{tag}{string to prefix output}
+}
+\value{
+nz_fc_co raw count object with no lines summing to zeros
+}
+\description{
+Parse featurecounts input as a follow-on from standard nf-core/rnaseq pipeline using STAR-Salmon (v3.3 currently)
+}