Single cell whole genome sequencing from Funnell, O'Flanagan, Williams et al

<p>This repository provides the processed data necessary to reproduce the results from: &quot;Single cell genomic variation induced by mutational processes in cancer<strong> </strong><em>Funnell,&nbsp;O&rsquo;Flanagan, Williams et al</em>&quot;</p> <p>This includes the following:</p> <ul> <li>Single cell whole genome sequencing <ul> <li>Allele specific copy number profiles</li> <li>SNV counts per cell</li> <li>Structural variant counts per cell</li> <li>QC metrics</li> <li>clone assignments</li> <li>phylogenetic trees computed with sitka</li> <li>benchmarking results vs other methods</li> </ul> </li> <li>bulk whole genome sequencing <ul> <li>copy number profiles</li> <li>SNVs</li> </ul> </li> <li>10X single cell RNA sequencing <ul> <li>count matrices</li> <li>seurat Rdata objects</li> </ul> </li> <li>analysis tables <ul> <li>downstream processed results used to generate figures</li> </ul> </li> <li>oxford nanopore <ul> <li>phasing results</li> </ul> </li> </ul> <p>&nbsp;</p> <p>For further information please feel free to get in touch with Marc Williams (william1 [at] mskcc.org)</p> <p>&nbsp;</p>