Resources

Next-generation Neuropathology

Web-based implementation of our DNA methylation-based classification system for central nervous system tumors. This classification system uses machine learning to turn patient-derived profiles into an accurate diagnosis. It is freely available and has become routine clinical assay that has been applied in tens-of-thousands of patients around the world.

https://www.molecularneuropathology.org

Copy-number variation analysis from methylation arrays

The conumee package enables “off-label” copy-number variation calling from Illumina DNA methylation arrays. This added information is of importance for the classification of many types of brain tumors and replaces additional, often costly and laborious assays. The original version of conumee is available on Bioconductor. Conumee 2.0 is available on GitHub.

https://github.com/hovestadtlab/conumee2

Anaysis of bisulfite sequencing data

methylCtools is a lightweight and versatile tool for the analysis of bisulfite-converted sequencing data. Bisulfite conversion is the gold-standard for quantifying CpG methylation and single basepair resolution. methylCtools wraps around popular tools like BWA and Samtools to provide both speed and functionality.

https://github.com/hovestadt/methylCtools

Single-cell transcriptome datasets

All our published single-cell transcriptome datasets are available through GEO to enable secondary analyses. Please get in touch with potential questions or comments.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119926