bioRxivBioinformatics
Rawcopy: Improved copy number analysis with Affymetrix arrays
Abstract
Rawcopy is an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). It uses data from a large number of reference samples to produce log ratio for total copy number analysis and B-allele frequency for allele-specific copy number and heterozygosity analysis. Rawcopy achieves higher signal-to-noise ratio than commonly used free and proprietary alternatives, leading to improved identification of copy number alterations. In addition, Rawcopy visualises each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states.
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Detecting copy number alterations in RNA-Seq using SuperFreq
Christoffer Flensburg, Alicia Oshlack, Ian J. Majewski·BioinformaticsPeer-reviewed·Jun 15, 2021
- CoFrEE: An Application to Estimate DNA Copy Number from Genome-wide RNA Expression Data
Anita Gaenko, Dipankar Ray, Derek J. Nancarrow·bioRxiv·Aug 25, 2023
- Minimum Error Calibration and Normalization for Genomic Copy Number Analysis
Bo Gao, Michael Baudis·GenomicsPeer-reviewed·May 13, 2020
- HandyCNV: Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH
Jinghang Zhou, Liyuan Liu, … Yuangang Shi·bioRxiv·Apr 5, 2021
- ClinCNV: novel method for allele-specific somatic copy-number alterations detection
German M. Demidov, Stephan Ossowski·bioRxiv·Nov 11, 2019
- Allele-specific multi-sample copy number segmentation
Edith M. Ross, Kerstin Haase, … Florian M. Markowetz·bioRxiv·Jul 20, 2017