Package: PeakSegDP 2024.1.24
PeakSegDP: Dynamic Programming Algorithm for Peak Detection in ChIP-Seq Data
A quadratic time dynamic programming algorithm can be used to compute an approximate solution to the problem of finding the most likely changepoints with respect to the Poisson likelihood, subject to a constraint on the number of segments, and the changes which must alternate: up, down, up, down, etc. For more info read <http://proceedings.mlr.press/v37/hocking15.html> "PeakSeg: constrained optimal segmentation and supervised penalty learning for peak detection in count data" by TD Hocking et al, proceedings of ICML2015.
Authors:
PeakSegDP_2024.1.24.tar.gz
PeakSegDP_2024.1.24.zip(r-4.5)PeakSegDP_2024.1.24.zip(r-4.4)PeakSegDP_2024.1.24.zip(r-4.3)
PeakSegDP_2024.1.24.tgz(r-4.4-x86_64)PeakSegDP_2024.1.24.tgz(r-4.4-arm64)PeakSegDP_2024.1.24.tgz(r-4.3-x86_64)PeakSegDP_2024.1.24.tgz(r-4.3-arm64)
PeakSegDP_2024.1.24.tar.gz(r-4.5-noble)PeakSegDP_2024.1.24.tar.gz(r-4.4-noble)
PeakSegDP_2024.1.24.tgz(r-4.4-emscripten)PeakSegDP_2024.1.24.tgz(r-4.3-emscripten)
PeakSegDP.pdf |PeakSegDP.html✨
PeakSegDP/json (API)
NEWS
| # Install 'PeakSegDP' in R: |
| install.packages('PeakSegDP', repos = c('https://tdhock.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tdhock/peaksegdp/issues
- H3K36me3.AM.immune.19 - Several ChIP-seq profiles, some of which have few data points
- H3K36me3.TDH.other.chunk3.cluster4 - 8 profiles of H3K36me3 data
- H3K4me3.TDH.immune.chunk12.cluster4 - Histone ChIP-seq data, 26 samples, chr1 subset
- chr11ChIPseq - ChIP-seq aligned read coverage for 4 samples on a subset of chr11
- chr11first - Counts of first base of aligned reads
Last updated 10 months agofrom:618128bb81. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-win-x86_64 | OK | Nov 20 2024 |
| R-4.5-linux-x86_64 | OK | Nov 20 2024 |
| R-4.4-win-x86_64 | OK | Nov 20 2024 |
| R-4.4-mac-x86_64 | OK | Nov 20 2024 |
| R-4.4-mac-aarch64 | OK | Nov 20 2024 |
| R-4.3-win-x86_64 | OK | Nov 20 2024 |
| R-4.3-mac-x86_64 | OK | Nov 20 2024 |
| R-4.3-mac-aarch64 | OK | Nov 20 2024 |
Exports:cDPAgetPathPeakSegDPPoissonLoss
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calc grad list | calc.grad.list |
| calc loss from lp list | calc.loss.from.lp.list |
| calc loss list | calc.loss.list |
| cDPA | cDPA |
| ChIP-seq aligned read coverage for 4 samples on a subset of chr11 | chr11ChIPseq |
| Counts of first base of aligned reads | chr11first |
| derivs | derivs |
| GeomTallRect | GeomTallRect |
| getPath | getPath |
| Several ChIP-seq profiles, some of which have few data points | H3K36me3.AM.immune.19 |
| 8 profiles of H3K36me3 data | H3K36me3.TDH.other.chunk3.cluster4 |
| Histone ChIP-seq data, 26 samples, chr1 subset | H3K4me3.TDH.immune.chunk12.cluster4 |
| PeakSegDP | PeakSegDP |
| phi list | phi.list |
| PoissonLoss | PoissonLoss |
| regression funs | regression.funs |
