Package: nucleoSim 1.35.0
Astrid Deschênes
nucleoSim: Generate synthetic nucleosome maps
This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.
Authors:
nucleoSim_1.35.0.tar.gz
nucleoSim_1.35.0.zip(r-4.5)nucleoSim_1.35.0.zip(r-4.4)nucleoSim_1.35.0.zip(r-4.3)
nucleoSim_1.35.0.tgz(r-4.4-any)nucleoSim_1.35.0.tgz(r-4.3-any)
nucleoSim_1.35.0.tar.gz(r-4.5-noble)nucleoSim_1.35.0.tar.gz(r-4.4-noble)
nucleoSim_1.35.0.tgz(r-4.4-emscripten)nucleoSim_1.35.0.tgz(r-4.3-emscripten)
nucleoSim.pdf |nucleoSim.html✨
nucleoSim/json (API)
NEWS
| # Install 'nucleoSim' in R: |
| install.packages('nucleoSim', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/arnauddroitlab/nucleosim/issues
On BioConductor:nucleoSim-1.35.0(bioc 3.21)nucleoSim-1.34.0(bioc 3.20)
geneticssequencingsoftwarestatisticalmethodalignmentbioconductornucleosome-mapsnucleosomessimulationsimulatorsynthetic-nucleosomes
Last updated 2 months agofrom:334622c8d8. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 27 2024 |
| R-4.5-win | NOTE | Nov 27 2024 |
| R-4.5-linux | NOTE | Nov 27 2024 |
| R-4.4-win | NOTE | Nov 27 2024 |
| R-4.4-mac | NOTE | Nov 27 2024 |
| R-4.3-win | OK | Nov 27 2024 |
| R-4.3-mac | OK | Nov 27 2024 |
Exports:syntheticNucMapFromDistsyntheticNucReadsFromDistsyntheticNucReadsFromMap
Dependencies:BiocGenericsgenericsIRangesS4Vectors
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| nucleoSim: Generate synthetic nucleosome maps | nucleoSim-package nucleoSim |
| Generate a graph of a synthetic nucleosome map | plot.syntheticNucMap |
| Generate a graph of a synthetic nucleosome map containing forward and reverse reads | plot.syntheticNucReads |
| Generate a synthetic nucleosome map containing complete sequences | syntheticNucMapFromDist |
| Generate a synthetic nucleosome map containing forward and reverse reads (paired-end reads) | syntheticNucReadsFromDist |
| Generate a synthetic nucleosome map containing forward and reverse reads | syntheticNucReadsFromMap |
