@@ -936,7 +936,7 @@ TCGAquery_recount2<-function(project, tissue=c()){

 #' @description

 #'   Retrieve open access ATAC-seq files from GDC server

 #'  https://gdc.cancer.gov/about-data/publications/ATACseq-AWG

-#'  Manifest available at: https://gdc.cancer.gov/files/public/file/ATACseq-AWG_Open_GDC-Manifest.txt

+#'  Manifest available at: https://gdc.cancer.gov/system/files/public/file/ATACseq-AWG_Open_GDC-Manifest.txt

 #' @param tumor a valid tumor

 #' @param file.type Write maf file into a csv document

 #' @export

@@ -955,7 +955,7 @@ GDCquery_ATAC_seq <- function(

         file.type = NULL

 ) {

     isServeOK()

-    results <- readr::read_tsv("https://gdc.cancer.gov/files/public/file/ATACseq-AWG_Open_GDC-Manifest.txt")

+    results <- readr::read_tsv("https://gdc.cancer.gov/system/files/public/file/ATACseq-AWG_Open_GDC-Manifest.txt")

     if(!is.null(tumor)) results <- results[grep(tumor,results$filename,ignore.case = TRUE),]

     if(!is.null(file.type))  results <- results[grep(file.type,results$filename,ignore.case = TRUE),]

@@ -21,7 +21,7 @@ knitr::opts_knit$set(progress = FALSE)

 ---

-```{r message=FALSE, warning=FALSE, include=FALSE}

+```{r libs, message=FALSE, warning=FALSE, include=FALSE}

 library(TCGAbiolinks)

 library(SummarizedExperiment)

 library(dplyr)

@@ -119,7 +119,7 @@ Please, note that these tables are still incomplete.

 ## Harmonized data options 

-```{r, echo=FALSE}

+```{r Harmonized_data_options, echo=FALSE}

 datatable(

     readr::read_csv("https://docs.google.com/spreadsheets/d/1f98kFdj9mxVDc1dv4xTZdx8iWgUiDYO-qiFJINvmTZs/export?format=csv&gid=2046985454",col_types = readr::cols()),

     filter = 'top',

@@ -216,7 +216,7 @@ datatable(

 This example shows how the user can search for breast cancer Raw Sequencing Data ("Controlled") 

 and verify the name of the files and the barcodes associated with it.

-```{r message=FALSE, warning=FALSE}

+```{r queries,message=FALSE, warning=FALSE}

 query <- GDCquery(

     project = "TCGA-ACC", 

     data.category = "Sequencing Reads",

@@ -299,8 +299,8 @@ datatable(

 If you want to get the manifest file from the query object you can use the function *getManifest*. If you 

 set save to `TRUE` a txt file that can be used with GDC-client Data transfer tool (DTT) or with its GUI version [ddt-ui](https://github.com/NCI-GDC/dtt-ui) will be created.

-```{r message=FALSE, warning=FALSE}

-getManifest(query,save = FALSE) 

+```{r get_manifest, message = FALSE, warning = FALSE}

+getManifest(query, save = FALSE) 

 ```

 # ATAC-seq data

@@ -310,7 +310,6 @@ Also, for more details, you can check an ATAC-seq workshop at http://rpubs.com/t

 The list of file available is below:

 ```{r message=FALSE, warning=FALSE}

-

 datatable(

     getResults(TCGAbiolinks:::GDCquery_ATAC_seq())[,c("file_name","file_size")], 

     filter = 'top',

@@ -320,13 +319,12 @@ datatable(

 ```

 You can use the function `GDCquery_ATAC_seq` filter the manifest table and use `GDCdownload` to save the data locally.

-```{r message=FALSE, warning=FALSE,eval = FALSE}

+```{r GDCquery_ATAC_seq, message=FALSE, warning=FALSE,eval = FALSE}

 query <- TCGAbiolinks:::GDCquery_ATAC_seq(file.type = "rds") 

 GDCdownload(query, method = "client")

 query <- TCGAbiolinks:::GDCquery_ATAC_seq(file.type = "bigWigs") 

 GDCdownload(query, method = "client")

-

 ```

 # Summary of available files per patient

@@ -334,7 +332,7 @@ GDCdownload(query, method = "client")

 Retrieve the numner of files under each data_category + data_type + experimental_strategy + platform.

 Almost like https://portal.gdc.cancer.gov/exploration

-```{r message=FALSE, warning=FALSE,eval = TRUE}

+```{r getSampleFilesSummary, message=FALSE, warning=FALSE,eval = TRUE}

 tab <-  getSampleFilesSummary(project = "TCGA-ACC")

 datatable(

     head(tab),