Data Catalog

Description from Figshare: "Table S1. Massively Parallel Sequencing (MPS) metrics and cancer sample characteristics."

Description from Figshare: "Table S6. Copy number alterations (CNAs) in cancer genes identified by whole exome sequencing (WES) and/or initial panel sequencing. Each sheet is a different tumor sample."

Description from Figshare: "Supplementary Table 1: Next-generation sequencing (MSK-IMPACT) gene panel"

Summary from GEO: "We have previously shown that Okazaki fragments in Saccharomyces cerevisiae are sized according to the chromatin repeat. Here we demonstrate that nucleosome positioning is rapidly established on newly synthesized DNA. Using deep sequencing, we demonstrate that ATP-dependent chromatin remodeling enzymes, Isw1 and Chd1, collaborate with histone chaperones, such as CAF-1 and Rtt106,...

Description from EMBL-EBI: "To uncover, in an unbiased fashion, which elements of the 18 kb translocated region control EVI1 transcription, we devised a CRISPR/Cas9-based enhancer scanning approach. We considered all possible sgRNA target sites containing a canonical Cas9 PAM site (NGG) on both strands of the minimal 18 kb translocated region. Deep-sequencing libraries were generated by PCR amplification...

Description from GitHub: "A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library HTSJDK to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM and VCF. As of version 3.0, Picard requires Java 1.17."

Description from GitHub: "AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number algorithm for paired end sequencing. We do not offer support for WXS analysis, please contact the authors of ASCAT here. For details of the underlying algorithm please see the ASCAT site. "

Description from GitHub: "An installation helper, perl wrapper and the R program Battenberg which detects subclonality and copy number in matched NGS data."

Description from GitHub: "iCallSV is a Python library and command-line software toolkit to call structural aberrations from Next Generation DNA sequencing data. Behind the scenes it uses Delly2 to do structural variant calling. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina."

Description from GitHub: "To convert a VCF into a MAF, each variant must be mapped to only one of all possible gene transcripts/isoforms that it might affect. But even within a single isoform, a Missense_Mutation close enough to a Splice_Site, can be labeled as either in MAF format, but not as both. This selection of a single effect per variant, is often subjective. And that's what this project...