Total Aberration Index | Modified Total Aberration Index | Copy Number Aberration | Counting Altered Base segments | Counting Number of Break Points | Fraction of Genome Altered
Package: CINmetrics 0.1.0
Vishal H. Oza
CINmetrics: Calculate Chromosomal Instability Metrics
Implement various chromosomal instability metrics. 'CINmetrics' (Chromosomal INstability metrics) provides functions to calculate various chromosomal instability metrics on masked Copy Number Variation(CNV) data at individual sample level. The chromosomal instability metrics have been implemented as described in the following studies: Baumbusch LO et al. 2013 <doi:10.1371/journal.pone.0054356>, Davidson JM et al. 2014 <doi:10.1371/journal.pone.0079079>, Chin SF et al. 2007 <doi:10.1186/gb-2007-8-10-r215>.
Authors:
CINmetrics_0.1.0.tar.gz
CINmetrics_0.1.0.zip(r-4.7-any)CINmetrics_0.1.0.zip(r-4.6-any)CINmetrics_0.1.0.zip(r-4.5-any)
CINmetrics_0.1.0.tgz(r-4.6-any)CINmetrics_0.1.0.tgz(r-4.5-any)
CINmetrics_0.1.0.tar.gz(r-4.7-any)CINmetrics_0.1.0.tar.gz(r-4.6-any)
CINmetrics_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CINmetrics/json (API)
| # Install 'CINmetrics' in R: |
| install.packages('CINmetrics', repos = c('https://vishaloza.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- maskCNV_BRCA - Breast Cancer Data from TCGA Data Release 25.0 GDC Product: Data Release Date: July 22, 2020 Masked Copy Number variation data for Breast Cancer for 10 unique samples selected randomly from TCGA
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:7e0cfc5303. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 132 | ||
| source / vignettes | OK | 145 | ||
| linux-release | OK | 130 | ||
| macos-release | OK | 89 | ||
| macos-oldrel | OK | 82 | ||
| windows-devel | OK | 61 | ||
| windows-release | OK | 53 | ||
| windows-oldrel | OK | 67 | ||
| wasm-release | OK | 87 |
Exports:CINmetricscnacountingBaseSegmentscountingBreakPointsfgataitaiModified
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CINmetrics | CINmetrics |
| Copy Number Aberration | cna |
| countingBaseSegments | countingBaseSegments |
| countingBreakPoints | countingBreakPoints |
| Fraction Genome Altered | fga |
| Breast Cancer Data from TCGA Data Release 25.0 GDC Product: Data Release Date: July 22, 2020 Masked Copy Number variation data for Breast Cancer for 10 unique samples selected randomly from TCGA | maskCNV_BRCA |
| Total Aberration Index | tai |
| Modified Total Aberration Index | taiModified |