EaCoN Easy Copy Number !
| Main Author: | JOB Bastien |
|---|---|
| Other Authors: | DAYRIS Thibault, GAUTHERET Daniel |
| Format: | info software Journal |
| Terbitan: |
, 2018
|
| Subjects: | |
| Online Access: |
https://zenodo.org/record/5494853 |
Daftar Isi:
- EaCoN Easy Copy Number ! DESCRIPTION EaCoN aims to be an all-packed in, user-friendly solution to perform relative or absolute copy-number analysis for multiple sources of data, with three different segmenters available (and corresponding three copy-number modelization methods). It consists in a series of R packages that perform such type of analysis, from raw CEL files of Affymetrix microarrays (GenomeWide snp6, OncoScan, CytoScan 750K, CytoScan HD) or from aligned reads as BAMs for WES (whole exome sequencing). Code and vignette are available at https://github.com/gustaveroussy/EaCoN FEATURES Full R (no OS-, language-, nor shell-specific dependencies) Platform-independent (ie, the three most common ones : Linux, Windows and OSX) Support of multiple sources of data : Affymetrix (homo sapiens) Genomide SNP6 CytoScan 750k CytoScan HD OncoScan / OncoScan_CNV WES (any species) Any design for which a capture BED and known genome are available Full workflow analysis, from the raw data to an annotated HTML report : L2R and BAF normalization from raw data using Affymetrix Power Tools (binaries, embedded) for Affymetrix arrays and the rawcopy BAF normalization methods for CytoScan and SNP6 arrays internal methods for WES data L2R and BAF bivariate segmentation using ASCAT (recommended), FACETS or SEQUENZA L2R profile centralization L2R profile CNA calling Generation of results as tables and plots Generation of a portable and interactive HTML report (for hs, mm and rn species at the moment) Total (TCN) and allele-specific copy number (ASCN), ploidy and cellularity estimations using ASCAT (recommended), FACETS or SEQUENZA for both WES and arrays (except for SNP6 arrays for the two latter) Required annotations for Affymetrix data provided (via additional packages) Pre-computed normalization (GC%, wave) tracks provided for arrays (either) Few functions to call Few parameters Recommended guidelines provided for supported microarray designs, as well as for WES
- This repo consists in R data packages needed for Affymetrix CNA microarray analysis (OncoScan, OncoScan_CNV, CytoScanHD, CytoScan_750k