Package: falconx 0.2
Hao Chen
falconx: Finding Allele-Specific Copy Number in Whole-Exome Sequencing Data
This is a method for Allele-specific DNA Copy Number profiling for whole-Exome sequencing data. Given the allele-specific coverage and site biases at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number. It requires, as input, the read counts for each variant allele in a pair of case and control samples, as well as the site biases. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual. The implemented method is based on the paper: Chen, H., Jiang, Y., Maxwell, K., Nathanson, K. and Zhang, N. (under review). Allele-specific copy number estimation by whole Exome sequencing.
Authors:
falconx_0.2.tar.gz
falconx_0.2.tar.gz(r-4.5-noble)falconx_0.2.tar.gz(r-4.4-noble)
falconx_0.2.tgz(r-4.4-emscripten)falconx_0.2.tgz(r-4.3-emscripten)
falconx.pdf |falconx.html✨
falconx/json (API)
# Install 'falconx' in R: |
install.packages('falconx', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- biasMatrix - Bias Matrix
- pos - Position
- readMatrix - Reads Matrix
- tauhat - Estimated Break Points
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 8 years agofrom:efa5f9d657. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 13 2024 |
R-4.5-linux-x86_64 | OK | Oct 13 2024 |
Exports:getASCN.xgetChangepoints.xview
Dependencies:
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Bias Matrix | biasMatrix |
Finding Allele-Specific Copy Number in Whole-Exome Sequencing Data | falconx |
Getting Allele-specific DNA Copy Number | getASCN.x |
Getting Change-points | getChangepoints.x |
Position (bp) | pos |
Reads Matrix | readMatrix |
Estimated Break Points | tauhat |
Viewing Data with Allele-specific Copy Number | view |