diff --git a/DESCRIPTION b/DESCRIPTION
index 410a79b..551fec2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: leapR
 Title: Layered enrichment analysis of pathways R
-Version: 0.99.8
+Version: 0.99.9
 Authors@R: c(
     person("Sara", "Gosline", email = "sara.gosline@pnnl.gov", role = c('aut',"cre"), comment = c(ORCID = "0000-0002-6534-4774")),
     person("Jason", "McDermott", email = "jason.mcdermott@pnnl.gov", role = "aut"),
@@ -17,7 +17,8 @@ biocViews:
   Proteomics,
   Pathways,
   GeneExpression, 
-  Transcriptomics
+  Transcriptomics,
+  Software
 Imports:
     stats,
     gplots,
@@ -30,7 +31,8 @@ Imports:
     stringr,
     tidyr,
     SummarizedExperiment, 
-    BiocStyle
+    BiocStyle,
+    BiocFileCache
 Suggests: 
     knitr,
     rmarkdown,
@@ -38,3 +40,4 @@ Suggests:
 VignetteBuilder: knitr
 License: MIT + file LICENSE
 Config/testthat/edition: 3
+URL: https://pnnl.github.io/leapR/
diff --git a/R/calcTTest.R b/R/calcTTest.R
index 095c35c..ca0df02 100644
--- a/R/calcTTest.R
+++ b/R/calcTTest.R
@@ -18,11 +18,15 @@
 #' @examples
 #'
 #'         library(leapR)
+#'         library(BiocFileCache)
+#'         
+#'         path <- tools::R_user_dir("leapR", which = "cache")
+#'         bfc <- BiocFileCache(path, ask = FALSE)
+#'         
 #'         url <- "https://api.figshare.com/v2/file/download/56536214"
-#'         tdata <- download.file(url,method='libcurl',destfile='transData.rda')
-#'         load('transData.rda')
-#'         p <- file.remove("transData.rda")
-#'
+#'         tc <- bfcadd(bfc, "tdat", fpath = url)
+#'         load(tc)
+#'         
 #'         # read in the pathways
 #'         data("ncipid")
 #'
diff --git a/R/cluster_enrichment.R b/R/cluster_enrichment.R
index d1f3120..7e76adf 100644
--- a/R/cluster_enrichment.R
+++ b/R/cluster_enrichment.R
@@ -19,12 +19,14 @@
 #' @export
 #' @examples
 #'         library(leapR)
-#'
-#'         # read in the example transcriptomic data
+#'         library(BiocFileCache)
+#'         
+#'         path <- tools::R_user_dir("leapR", which = "cache")
+#'         bfc <- BiocFileCache(path, ask = FALSE)
+#'         
 #'         url <- "https://api.figshare.com/v2/file/download/56536214"
-#'         tdata <- download.file(url,method='libcurl',destfile='transData.rda')
-#'         load('transData.rda')
-#'         p <- file.remove("transData.rda")
+#'         tc <- bfcadd(bfc, "tdat", fpath = url)
+#'         load(tc)
 #'
 #'         # read in the pathways
 #'         data("ncipid")
diff --git a/R/combine_omics.R b/R/combine_omics.R
index 101d595..78dbbcc 100644
--- a/R/combine_omics.R
+++ b/R/combine_omics.R
@@ -18,23 +18,21 @@
 #'
 #' @examples
 #'         library(leapR)
-#'         url <- 'https://api.figshare.com/v2/file/download/56536217'
-#'
-#'         pdata <- download.file(url,method='libcurl',destfile='protData.rda')
-#'         load('protData.rda')
-#'         p <- file.remove("protData.rda")
-#'
+#'         library(BiocFileCache)
+#'         path <- tools::R_user_dir("leapR", which = "cache")
+#'         bfc <- BiocFileCache(path, ask = FALSE)
+#'         
+#'         url <- "https://api.figshare.com/v2/file/download/56536217"
+#'         pc <- bfcadd(bfc, "pdat", fpath = url)
+#'         load(pc)
+#'         
 #'         url <- "https://api.figshare.com/v2/file/download/56536214"
-#'         tdata <- download.file(url,method='libcurl',destfile='transData.rda')
-#'         load('transData.rda')
-#'         p <- file.remove("transData.rda")
-#'
-#'         url <- 'https://api.figshare.com/v2/file/download/56536211'
-#'         phdata<-download.file(url,method='libcurl',destfile = 'phosData.rda')
-#'         #phosphodata<-read.csv("phdata",check.names=FALSE,row.names=1)
-#'         load('phosData.rda')
-#'         p <- file.remove('phosData.rda')# read in the example protein data
-#'
+#'         tc <- bfcadd(bfc, "tdat", fpath = url)
+#'         load(tc)
+#'         
+#'         url <- "https://api.figshare.com/v2/file/download/56536211"
+#'         phc <- bfcadd(bfc, "phdat", fpath = url)
+#'         load(phc)
 #'
 #'         # merge the three datasets by rows and add prefix tags for
 #'         # different omics types
diff --git a/R/enrichment_in_groups.R b/R/enrichment_in_groups.R
index b82cc45..4d92940 100644
--- a/R/enrichment_in_groups.R
+++ b/R/enrichment_in_groups.R
@@ -18,6 +18,7 @@
 #' to log your data before calling. NOTE: if you do not call `suppressWarnings` then
 #' the KS test will warn you about ties.
 #' @param minsize minimum size of set
+#' @param log_transformed Set to TRUE if data is already log-transformed
 #' @param mapping_column column name of mapping identifiers
 #' @param abundance_column columns mapping abundance, either in the `assay`
 #' matrix or `rowData`
@@ -114,7 +115,7 @@ enrichment_in_groups <- function(geneset,
       names(backvals) <- backlist#[-group_ind]
       in_back <- length(backvals)
       
-      outgroup_mean = mean(backvals[-group_ind], na.rm = T)
+      outgroup_mean = mean(backvals[-group_ind], na.rm = TRUE)
       
       in_path <- length(in_group) #how many left after na.rm
       if ((in_path > minsize) & (any(!is.na(in_path))) &
diff --git a/R/leapR-package.R b/R/leapR-package.R
index ad09996..f82de0d 100644
--- a/R/leapR-package.R
+++ b/R/leapR-package.R
@@ -143,14 +143,14 @@
 #' \cr
 #' @examples
 #'         library(leapR)
-#'
-#'  # read in the example abundance data
-#'  # read in the example transcriptomic data
-#'  tdata <- download.file("https://api.figshare.com/v2/file/download/56536214",
-#'       method='libcurl',destfile='transData.rda')
-#'  load('transData.rda')
-#'  p <- file.remove("transData.rda")
-#'
+#'         library(BiocFileCache)
+#'         
+#'         path <- tools::R_user_dir("leapR", which = "cache")
+#'         bfc <- BiocFileCache(path, ask = FALSE)
+#'         
+#'         url <- "https://api.figshare.com/v2/file/download/56536214"
+#'         tc <- bfcadd(bfc, "tdat", fpath = url)
+#'         load(tc)
 #'  # read in the pathways
 #'  data("ncipid")
 #'
diff --git a/R/leapR.R b/R/leapR.R
index 05318c4..4b53700 100644
--- a/R/leapR.R
+++ b/R/leapR.R
@@ -140,13 +140,14 @@
 #' \cr
 #' @examples
 #'         library(leapR)
-#'
-#'  # read in the example abundance data
-#'  # read in the example transcriptomic data
-#'  tdata <- download.file("https://api.figshare.com/v2/file/download/56536214",
-#'       method='libcurl',destfile='transData.rda')
-#'  load('transData.rda')
-#'  p <- file.remove("transData.rda")
+#'         library(BiocFileCache)
+#'         
+#'         path <- tools::R_user_dir("leapR", which = "cache")
+#'         bfc <- BiocFileCache(path, ask = FALSE)
+#'         
+#'         url <- "https://api.figshare.com/v2/file/download/56536214"
+#'         tc <- bfcadd(bfc, "tdat", fpath = url)
+#'         load(tc)
 #'
 #'  # read in the pathways
 #'  data("ncipid")
diff --git a/leapR.Rproj b/leapR.Rproj
new file mode 100644
index 0000000..eaa6b81
--- /dev/null
+++ b/leapR.Rproj
@@ -0,0 +1,18 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace
diff --git a/man/calcTTest.Rd b/man/calcTTest.Rd
index 94a5a27..64a0eb5 100644
--- a/man/calcTTest.Rd
+++ b/man/calcTTest.Rd
@@ -27,11 +27,15 @@ append results to ExpressionSet with two extra columns: `pvalue` and
 \examples{
 
         library(leapR)
+        library(BiocFileCache)
+        
+        path <- tools::R_user_dir("leapR", which = "cache")
+        bfc <- BiocFileCache(path, ask = FALSE)
+        
         url <- "https://api.figshare.com/v2/file/download/56536214"
-        tdata <- download.file(url,method='libcurl',destfile='transData.rda')
-        load('transData.rda')
-        p <- file.remove("transData.rda")
-
+        tc <- bfcadd(bfc, "tdat", fpath = url)
+        load(tc)
+        
         # read in the pathways
         data("ncipid")
 
diff --git a/man/cluster_enrichment.Rd b/man/cluster_enrichment.Rd
index c9428ef..1d4b487 100644
--- a/man/cluster_enrichment.Rd
+++ b/man/cluster_enrichment.Rd
@@ -36,12 +36,14 @@ a list of results matrices in the order of the input clusters.
 }
 \examples{
         library(leapR)
-
-        # read in the example transcriptomic data
+        library(BiocFileCache)
+        
+        path <- tools::R_user_dir("leapR", which = "cache")
+        bfc <- BiocFileCache(path, ask = FALSE)
+        
         url <- "https://api.figshare.com/v2/file/download/56536214"
-        tdata <- download.file(url,method='libcurl',destfile='transData.rda')
-        load('transData.rda')
-        p <- file.remove("transData.rda")
+        tc <- bfcadd(bfc, "tdat", fpath = url)
+        load(tc)
 
         # read in the pathways
         data("ncipid")
diff --git a/man/combine_omics.Rd b/man/combine_omics.Rd
index 74f0e50..d359663 100644
--- a/man/combine_omics.Rd
+++ b/man/combine_omics.Rd
@@ -31,23 +31,21 @@ adds prefix tags to the ids.
 }
 \examples{
         library(leapR)
-        url <- 'https://api.figshare.com/v2/file/download/56536217'
-
-        pdata <- download.file(url,method='libcurl',destfile='protData.rda')
-        load('protData.rda')
-        p <- file.remove("protData.rda")
-
+        library(BiocFileCache)
+        path <- tools::R_user_dir("leapR", which = "cache")
+        bfc <- BiocFileCache(path, ask = FALSE)
+        
+        url <- "https://api.figshare.com/v2/file/download/56536217"
+        pc <- bfcadd(bfc, "pdat", fpath = url)
+        load(pc)
+        
         url <- "https://api.figshare.com/v2/file/download/56536214"
-        tdata <- download.file(url,method='libcurl',destfile='transData.rda')
-        load('transData.rda')
-        p <- file.remove("transData.rda")
-
-        url <- 'https://api.figshare.com/v2/file/download/56536211'
-        phdata<-download.file(url,method='libcurl',destfile = 'phosData.rda')
-        #phosphodata<-read.csv("phdata",check.names=FALSE,row.names=1)
-        load('phosData.rda')
-        p <- file.remove('phosData.rda')# read in the example protein data
-
+        tc <- bfcadd(bfc, "tdat", fpath = url)
+        load(tc)
+        
+        url <- "https://api.figshare.com/v2/file/download/56536211"
+        phc <- bfcadd(bfc, "phdat", fpath = url)
+        load(phc)
 
         # merge the three datasets by rows and add prefix tags for
         # different omics types
diff --git a/man/enrichment_in_groups.Rd b/man/enrichment_in_groups.Rd
index 6392c4c..c839d02 100644
--- a/man/enrichment_in_groups.Rd
+++ b/man/enrichment_in_groups.Rd
@@ -12,6 +12,7 @@ enrichment_in_groups(
   method = "fishers",
   minsize = 5,
   mapping_column = NULL,
+  log_transformed = FALSE,
   abundance_column = NULL,
   randomize = FALSE,
   silence_try_errors = TRUE
@@ -35,6 +36,8 @@ the KS test will warn you about ties.}
 
 \item{mapping_column}{column name of mapping identifiers}
 
+\item{log_transformed}{Set to TRUE if data is already log-transformed}
+
 \item{abundance_column}{columns mapping abundance, either in the `assay`
 matrix or `rowData`}
 
diff --git a/man/leapR-package.Rd b/man/leapR-package.Rd
index 41c7aa5..821a41b 100644
--- a/man/leapR-package.Rd
+++ b/man/leapR-package.Rd
@@ -6,6 +6,13 @@
 \title{leapR: Layered enrichment analysis of pathways R}
 \description{
 leapR is a package that identifies pathways that are enriched across diverse 'omics experiments. It leverages any tabular expression data (proteomics, transcriptomics) using the `SummarizedExperiment` object. It works with any pathway in the .gct file format.
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://pnnl.github.io/leapR/}
+}
+
 }
 \author{
 \strong{Maintainer}: Sara Gosline \email{sara.gosline@pnnl.gov} (\href{https://orcid.org/0000-0002-6534-4774}{ORCID})
@@ -13,6 +20,7 @@ leapR is a package that identifies pathways that are enriched across diverse 'om
 Authors:
 \itemize{
   \item Jason McDermott \email{jason.mcdermott@pnnl.gov}
+  \item Jeremy Jacobson \email{jeremy.jacobson@pnnl.gov}
 }
 
 Other contributors:
diff --git a/man/leapR.Rd b/man/leapR.Rd
index a448e22..3bd6fb2 100644
--- a/man/leapR.Rd
+++ b/man/leapR.Rd
@@ -151,13 +151,14 @@ pathway.
 }
 \examples{
         library(leapR)
-
- # read in the example abundance data
- # read in the example transcriptomic data
- tdata <- download.file("https://api.figshare.com/v2/file/download/56536214",
-      method='libcurl',destfile='transData.rda')
- load('transData.rda')
- p <- file.remove("transData.rda")
+        library(BiocFileCache)
+        
+        path <- tools::R_user_dir("leapR", which = "cache")
+        bfc <- BiocFileCache(path, ask = FALSE)
+        
+        url <- "https://api.figshare.com/v2/file/download/56536214"
+        tc <- bfcadd(bfc, "tdat", fpath = url)
+        load(tc)
 
  # read in the pathways
  data("ncipid")
diff --git a/vignettes/examples.Rmd b/vignettes/examples.Rmd
index 1dbcd3a..4570d83 100644
--- a/vignettes/examples.Rmd
+++ b/vignettes/examples.Rmd
@@ -31,6 +31,7 @@ library(ggplot2)
 library(dplyr)
 library(tibble)
 library(stringr)
+library(BiocFileCache)
 ```
 
 #  Example data
@@ -44,22 +45,23 @@ as example.
 
 This data can be loaded as follows:
 ```{r omicsdata, message=FALSE, warning=FALSE}
-url <- "https://api.figshare.com/v2/file/download/56536217"
-pdata <- download.file(url, method = "libcurl", destfile = "protData.rda")
-#  as.matrix()
-load("protData.rda")
 
-p <- file.remove("protData.rda")
+#currently using the BiocFileCache though i'm not sure it helps
+path <- tools::R_user_dir("leapR", which = "cache")
+bfc <- BiocFileCache(path, ask = FALSE)
+
+url <- "https://api.figshare.com/v2/file/download/56536217"
+pc <- bfcadd(bfc, "pdat", fpath = url)
+load(pc)
 
 url <- "https://api.figshare.com/v2/file/download/56536214"
-tdata <- download.file(url, method = "libcurl", destfile = "transData.rda")
-load("transData.rda")
-p <- file.remove("transData.rda")
+tc <- bfcadd(bfc, "tdat", fpath = url)
+load(tc)
 
 url <- "https://api.figshare.com/v2/file/download/56536211"
-phdata <- download.file(url, method = "libcurl", destfile = "phosData.rda")
-load("phosData.rda")
-p <- file.remove("phosData.rda")
+phc <- bfcadd(bfc, "phdat", fpath = url)
+load(phc)
+
 ```
 
 We also have local data we can load
diff --git a/vignettes/leapR.Rmd b/vignettes/leapR.Rmd
index 45d987c..35e0f6f 100644
--- a/vignettes/leapR.Rmd
+++ b/vignettes/leapR.Rmd
@@ -44,6 +44,7 @@ library(ggplot2)
 library(dplyr)
 library(tibble)
 library(stringr)
+library(BiocFileCache)
 ```
 
 # Introduction
@@ -149,22 +150,21 @@ as example.
 
 This data can be loaded as follows:
 ```{r omicsdata, message=FALSE, warning=FALSE, echo = FALSE}
-url <- "https://api.figshare.com/v2/file/download/56536217"
-pdata <- download.file(url, method = "libcurl", destfile = "protData.rda")
-#  as.matrix()
-load("protData.rda")
+#currently using the BiocFileCache though i'm not sure it helps
+path <-tools::R_user_dir("leapR", which = "cache")
+bfc <- BiocFileCache(path, ask = FALSE)
 
-p <- file.remove("protData.rda")
+url <- "https://api.figshare.com/v2/file/download/56536217"
+pc <- bfcadd(bfc, "pdat", fpath = url)
+load(pc)
 
 url <- "https://api.figshare.com/v2/file/download/56536214"
-tdata <- download.file(url, method = "libcurl", destfile = "transData.rda")
-load("transData.rda")
-p <- file.remove("transData.rda")
+tc <- bfcadd(bfc, "tdat", fpath = url)
+load(tc)
 
 url <- "https://api.figshare.com/v2/file/download/56536211"
-phdata <- download.file(url, method = "libcurl", destfile = "phosData.rda")
-load("phosData.rda")
-p <- file.remove("phosData.rda")
+phc <- bfcadd(bfc, 'phdat', fpath =url)
+load(phc)
 ```
  
 ```{r show_pset_example}
diff --git a/vignettes/order-enrichment.Rmd b/vignettes/order-enrichment.Rmd
index 336e161..a2e3bad 100644
--- a/vignettes/order-enrichment.Rmd
+++ b/vignettes/order-enrichment.Rmd
@@ -31,17 +31,26 @@ library(ggplot2)
 library(dplyr)
 library(tibble)
 library(stringr)
+library(BiocFileCache)
 ```
 
 
 # Load our test proteomics dataset
 ```{r load data}
+
+
+#currently using the BiocFileCache though i'm not sure it helps
+path <- tools::R_user_dir("leapR", which = "cache")
+bfc <- BiocFileCache(path, ask = FALSE)
+
 url <- "https://api.figshare.com/v2/file/download/56536217"
-pdata <- download.file(url, method = "libcurl", destfile = "protData.rda")
+pd <- bfcadd(bfc, 'protdat', url)
+load(pd)
+#pdata <- download.file(url, method = "libcurl", destfile = "protData.rda")
 #  as.matrix()
-load("protData.rda")
+#load("protData.rda")
 
-p <- file.remove("protData.rda")
+#p <- file.remove("protData.rda")
 
 data(shortlist)
 data(longlist)
@@ -69,7 +78,9 @@ cor.res <- do.call(rbind,lapply(1:length(shortlist), function (i) {
     primary_columns = shortlist[i]
   )
   
-  colnames(protdata.enrichment.ks) <- paste('ks',colnames(protdata.enrichment.ks),sep='.')
+  colnames(protdata.enrichment.ks) <- paste('ks',
+                                            colnames(protdata.enrichment.ks),
+                                            sep = '.')
   
   
   protdata.enrichment.cs <- leapR::leapR(
@@ -79,7 +90,9 @@ cor.res <- do.call(rbind,lapply(1:length(shortlist), function (i) {
     assay_name = "proteomics",
     primary_columns = shortlist[i]
   )
-  colnames(protdata.enrichment.cs) <- paste('chisq',colnames(protdata.enrichment.cs),sep='.')
+  colnames(protdata.enrichment.cs) <- paste('chisq',
+                                            colnames(protdata.enrichment.cs),
+                                            sep = '.')
   
   protdata.enrichment.zt <- leapR::leapR(
     geneset = ncipid, "enrichment_in_order",
@@ -89,7 +102,9 @@ cor.res <- do.call(rbind,lapply(1:length(shortlist), function (i) {
     primary_columns = shortlist[i]
   )
   
-  colnames(protdata.enrichment.zt) <- paste('ztest',colnames(protdata.enrichment.zt),sep='.')
+  colnames(protdata.enrichment.zt) <- paste('ztest',
+                                            colnames(protdata.enrichment.zt),
+                                            sep = '.')
   
   paths <- rownames(protdata.enrichment.ks)
   allvals <- cbind(protdata.enrichment.cs[paths,],