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+---
+title: 'The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform,
+  from cancer multi-omics to single-cell RNA-seq'
+authors:
+- affiliation: '1, 2, 3'
+  name: Shixiang Wang
+  orcid: 0000-0001-9855-7357
+- affiliation: 1
+  name: Xuesong Liu
+  orcid: 0000-0002-7736-0077
+date: "24 July 2019"
+bibliography: paper.bib
+tags:
+- R
+- cancer genomics
+- data access
+affiliations:
+- index: 1
+  name: School of Life Science and Technology, ShanghaiTech University
+- index: 2
+  name: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences
+- index: 3
+  name: University of Chinese Academy of Sciences
+---
+
+# Summary
+
+UCSC Xena platform (https://xenabrowser.net/) provides unprecedented resource for public omics data [@goldman2019ucsc]
+from big projects like The Cancer Genome Atlas (TCGA) [@weinstein2013cancer], 
+International Cancer Genome Consortium Data Portal (ICGC) [@zhang2011international],
+The Cancer Cell Line Encyclopedia (CCLE) [@barretina2012cancer], or reserach groups like @mullighan2008genomic, @puram2017single.
+All available data types include single-nucleotide variants (SNVs), small insertions and deletions (INDELs), large structural variants, copy number variation (CNV), expression, DNA methylation, ATAC-seq signals, and phenotypic annotations. 
+
+Despite UCSC Xena platform itself allows users to explore and analyze data, it is hard
+for users to incorporate multiple datasets or data types, integrate the selected data with 
+popular analysis tools or homebrewed code, and reproduce analysis procedures.
+R language is well established and extensively used standard in statistical and bioinformatics research.
+Here, we introduce an R package UCSCXenaTools for enabling data retrieval, analysis integration and 
+reproducible research for omics data from UCSC Xena platform.
+
+Currently, UCSCXenaTools supports downloading over 1600 datasets from 10 data hubs of UCSC Xena platform
+as shown in the following table. Typically, downloading UCSC Xena datasets and loading them into R by UCSCXenaTools 
+is a workflow with generate, filter, query, download and prepare 5 steps, which are implemented as functions.
+They are very clear and easy to use and combine with other packages like dplyr [@wickham2015dplyr].
+Besides, UCSCXenaTools can also query and download subset of a target dataset, 
+this is particularly useful when
+user focus on studying one object like gene or protein. The key features are summarized in Figure 1.
+
+
+|Data hub       | Dataset count|URL                                |
+|:--------------|-------------:|:----------------------------------|
+|tcgaHub        |           879|https://tcga.xenahubs.net          |
+|gdcHub         |           449|https://gdc.xenahubs.net           |
+|publicHub      |           104|https://ucscpublic.xenahubs.net    |
+|pcawgHub       |            53|https://pcawg.xenahubs.net         |
+|toilHub        |            50|https://toil.xenahubs.net          |
+|singlecellHub  |            45|https://singlecell.xenahubs.net    |
+|icgcHub        |            23|https://icgc.xenahubs.net          |
+|pancanAtlasHub |            19|https://pancanatlas.xenahubs.net   |
+|treehouseHub   |            15|https://xena.treehouse.gi.ucsc.edu |
+|atacseqHub     |             9|https://atacseq.xenahubs.net       |
+
+![Overview of UCSCXenaTools](overview.png)
+
+# Acknowledgements
+
+We thank Christine Stawitz and Carl Ganz for their constructive comments.
+This package is based on R package [XenaR](https://github.com/mtmorgan/XenaR), thanks [Martin Morgan](https://github.com/mtmorgan) for his work.
+
+# References