ucscbrowser_human.Rmd

---
title: 'Human NeoCortex Track Hub for UCSC Genome Browser'
---

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table, th, td {
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  border-collapse: collapse;
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body {
text-align: justify}
.main-container {
  max-width: 1850px;
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<!-- Select a **gene/feature** from the **Count Data** table and then copy paste to **Genome Browser**.  -->

<!-- You can use the **Cluster** field to search for genes that are markers of Cell Types. -->

<!-- ### Count Data -->

<!-- ```{r echo=FALSE, include=FALSE} -->
<!-- knitr::opts_chunk$set(warning = FALSE, message = FALSE)  -->
<!-- library(DT) -->
<!-- library(knitr) -->
<!-- datax_atac <- read.table("files/atac_feature_metadata_human.tsv", header = T, sep = "\t", row.names = NULL) -->
<!-- datax_cage <- read.table("files/cage_feature_metadata_human.tsv", header = T, sep = "\t", row.names = NULL) -->
<!-- ``` -->

<!-- #### **ATAC-Seq** -->

<!-- <div align="center"> -->
<!-- ``` {r fig1, echo = FALSE, include=TRUE} -->
<!-- DT::datatable(datax_atac, class = 'display responsive nowrap', filter = 'top', options = list(scrollX = TRUE), rownames = FALSE) -->
<!-- ``` -->
<!-- </div> -->

<!-- #### **CAGE-Seq** -->

<!-- <div align="center"> -->
<!-- ``` {r fig2, echo = FALSE, include=TRUE} -->
<!-- DT::datatable(datax_cage, class = 'display responsive nowrap', filter = 'top', options = list(scrollX = TRUE), rownames = FALSE) -->
<!-- ``` -->
<!-- </div> -->

<!-- ### Genome Browser -->

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; This track hub was built by aggregated **scATAC-Seq** and **CAGE-Seq** reads of the human neocortex. You can query for positions, isoforms and genes to browse sequencing reads and ATAC-Seq and CAGE-Seq peaks. 

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; In order to download nucleotide sequences, simply go to **View** -> **DNA** ->  **get DNA**. 

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; See the [DolphinNext](https://dnext.dolphinnext.com/index.php?np=3&id=330) run for querying genes of interests on an aggregated gene expression and peaks data table, integrated to this UCSC Track Hub. Click to **Report** -> **UCSC Genome Browser**. 

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Please wait until the UCSC Genome Browser is fully loaded!

<div align="center">
  <iframe width='1650px' height='1000px' frameBorder='0' src='https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr18%3A32763856%2D32769639&hgsid=1537663415_EJ9iVP396eUrkO7TjpNYSzKTcnsb'>
    <p>Your browser does not support iframes</p>
  </iframe>
</div>