Package: scquantum 1.0.0
scquantum: Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing
Given bincount data from single-cell copy number profiling (segmented or unsegmented), estimates ploidy, and uses the ploidy estimate to scale the data to absolute copy numbers. Uses the modular quantogram proposed by Kendall (1986) <doi:10.1002/0471667196.ess2129.pub2>, modified by weighting segments according to confidence, and quantifying confidence in the estimate using a theoretical quantogram. Includes optional fused-lasso segmentation with the algorithm in Johnson (2013) <doi:10.1080/10618600.2012.681238>, using the implementation from glmgen by Arnold, Sadhanala, and Tibshirani.
Authors:
scquantum_1.0.0.tar.gz
scquantum_1.0.0.zip(r-4.5)scquantum_1.0.0.zip(r-4.4)scquantum_1.0.0.zip(r-4.3)
scquantum_1.0.0.tgz(r-4.4-x86_64)scquantum_1.0.0.tgz(r-4.4-arm64)scquantum_1.0.0.tgz(r-4.3-x86_64)scquantum_1.0.0.tgz(r-4.3-arm64)
scquantum_1.0.0.tar.gz(r-4.5-noble)scquantum_1.0.0.tar.gz(r-4.4-noble)
scquantum_1.0.0.tgz(r-4.4-emscripten)scquantum_1.0.0.tgz(r-4.3-emscripten)
scquantum.pdf |scquantum.html✨
scquantum/json (API)
| # Install 'scquantum' in R: |
| install.packages('scquantum', repos = c('https://alex-l-m.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:b6fcd39eef. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 07 2024 |
| R-4.5-win-x86_64 | OK | Nov 07 2024 |
| R-4.5-linux-x86_64 | OK | Nov 07 2024 |
| R-4.4-win-x86_64 | OK | Nov 07 2024 |
| R-4.4-mac-x86_64 | OK | Nov 07 2024 |
| R-4.4-mac-aarch64 | OK | Nov 07 2024 |
| R-4.3-win-x86_64 | OK | Nov 07 2024 |
| R-4.3-mac-x86_64 | OK | Nov 07 2024 |
| R-4.3-mac-aarch64 | OK | Nov 07 2024 |
Exports:ecf.global.maxexpected.peak.heightsgatirises.pluspurplel2e.normal.sdploidy.inferenceprof2invalsquantum.sdseg2invalssegment.summarizetf.dptimeseries.iodweighted.ecf
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Ploidy inference with quantogram | ploidy.inference |
