update Rshiny

Rshiny/data_trim.R

@@ -62,11 +62,11 @@ summary(as.factor(df$Chrom))
 <b>Citation</b><br>
   If you used the dataset for your research, please cite the following publication:
   <br>
-  Wojciech Rosikiewicz, Yang Liu, Ziwei Pan, Sheng Li,
-A  comprehensive comparison of tools for detecting DNA methylation using Nanopore long-read sequencing data,
-Genome Biology, btz877, 
+  Liu, Y., Rosikiewicz, W., Pan, Z. et al. 
+DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation. 
+Genome Biol 22, 295 (2021).,
 <a href=paperlink title="DOI" target="_blank">
-  https://doi.org/xxxx</a><br>
+  https://doi.org/10.1186/s13059-021-02510-z</a><br>
   <br>
 
   <br/>

Rshiny/global.R

@@ -12,7 +12,7 @@ column_names <-c('Chrom', 'Start', 'End', 'Strand', 'Dataset', 'BSseq_freq', 'BS
 df <- data.table::fread(input='./data/total.unique.tsv.bz2', sep="\t")
 
 data.table::setnames(df, column_names)
-df
+#df
 
 chr_order <- factor(df$Chrom, levels = c(paste("chr",1:22,sep=""),"chrX","chrY"))
 dataset_order <- factor(df$Dataset, levels = c("NA19240", "NA12878", "APL","K562"))

Rshiny/rsconnect/rshiny.jax.org/c-panz/rshiny_nanopore.dcf

@@ -5,10 +5,10 @@ account: c-panz
 server: rshiny.jax.org
 hostUrl: https://rshiny.jax.org/__api__
 appId: 162
-bundleId: 1105
+bundleId: 1172
 url: https://rshiny.jax.org/content/162/
-when: 1628389430.52753
-lastSyncTime: 1628389430.52763
+when: 1634676735.22697
+lastSyncTime: 1634676735.227
 asMultiple: FALSE
 asStatic: FALSE
 ignoredFiles: data/total.tsv.bz2|data/total.unique.tsv|data_trim.R

Rshiny/server.R

@@ -0,0 +1,63 @@
+function(input, output, session) {
+  library(shiny)
+  dataInput <- reactive({
+    #dataframe creation
+    df %>%
+      filter(Dataset %in% input$Dataset, 
+             Chrom %in% input$Chrom,
+             Strand %in% input$Strand,
+             Singleton %in% input$Singleton,
+             Genomic_location %in% input$Genomic_location, 
+             CpG_location %in% input$CpG_location,
+             CG_density %in% input$CG_density,
+             Repetitive_regions %in% input$Repetitive_regions)
+  })
+  output$table1 <- renderDT({
+    DT::datatable(dataInput())
+  })
+
+
+  # Reference: https://github.com/romanhaa/cerebroApp/blob/7fb55f08d1cb9611039e9b73f2859f3a61f4fd42/inst/shiny/v1.3/about/server.R
+  output[["about"]] <- renderText({
+    paste0(
+      '<b>Overview</b>
+      <br>
+      This application is an online DNA methylation database to display the DNA methylation levels detected by nanopore sequencing
+      and bisulfite sequencing data across different genomic contexts.
+      <br/>
+      Seven methylation calling tools are included in the dataset: Nanopolish, Megalodon, DeepSignal, Guppy, Tombo, METEORE, DeepMod
+      <br/>
+      Note: 
+      <br/>
+      1) All start coordinates in the application are 1-based, not 0-based.
+      <br/>
+      2) Only overlapped sites covered by >= 5 reads in BS-seq and >=3 reads in methylation calling tools are considered
+      <br/>
+      3) Genomic regions is annotated with promoter > exon > intron > intergenic regions(refer to intergenic) precedence
+      <br/>
+      4) Promoter is define as the 2000bp up an down of the transcriptional start codon
+      <br/>
+      <br>
+      <b>Funding</b>
+      <br>This study was funded and supported by the Jackson Laboratory.<br>
+      <br>
+      <b>Contact</b><br>
+      Ziwei Pan: <a href="mailto:ziwei.pan@jax.org">ziwei.pan@jax.org</a><br>
+      <br>
+      <b>Citation</b><br>
+      If you used the dataset for your research, please cite the following <a href=https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02510-z target="Link to publication">publication</a>:
+      <br>
+      Liu, Y., Rosikiewicz, W., Pan, Z. et al. 
+      DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation. 
+      Genome Biol 22, 295 (2021).,
+      <a href=https://doi.org/10.1186/s13059-021-02510-z title="DOI number" target="_blank">https://doi.org/10.1186/s13059-021-02510-z.</a><br>
+      <br>
+      <b>License</b><br>
+      The data presented here associated with the publication in the Citation section.
+      <br/>
+      The application is distributed under the terms of the <a href=https://opensource.org/licenses/MIT title="MIT license" target="_blank">MIT license.</a><br>
+      <br>'
+    )
+  })
+
+}