=============== The molecular landscape of cutaneous neurofibromas

This project is focused on analyzing the molecular landscape of cutaneous NF and is funded by the Children's Tumor Foundation. All available data and key analysis steps uploaded to http://www.synapse.org/cutaneousNF

To access the data you will need to register with Synapse and click through to get approval to use the data for your own research. One you are authenticated, there are numerous scripts provided here to facilitate analysis of the data. These scripts access the data through the Synapse R and Python Clients.

Data available for download

This project contains diverse types of high-throughput data. Links to the analysis of each type of data can be found here:

• Copy Number Alteration data from SNP OMNI Arrays
• Whole Genome Sequencing
• RNA-Sequencing
• iTRAQ Proteomics

Each dataset is described in more detail below.

SNP Arrays

SNP Array data collection is described on the wiki with files available as output from GenomeStudio. Files can be downloaded in their original form using the cnv_unprocessed_files function in bin/dermalNFData.R script available here.

Whole Genome Sequencing (WGS)

The WGS data was processed in numerous ways to compare and contrast various methods of calling variants and mutation calls. More details are available on the wiki.

RNA-Seq

RNA-Seq collection is described on the wiki with BAM files and RNA quantities available for download.

Gene matrices can be downloaded via various functions in bin/dermalNFData.R script available here.

Structure of this repository

Binaries used to process this data can be found in the binaries directory while specific analytical tasks can be found in the analysis directory.