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