Licensing and citing | Introduction | Loading r Rpackage("nucleoSim") package | Description | Synthetic Nucleosome Maps | Create a nucleosome map using syntheticNucMapFromDist() | Simulate hybridization data of Tiling Arrays | Synthetic Nucleosome Samples | Create a nucleosome sample using syntheticNucReadsFromDist() | Create a nucleosome sample using syntheticNucReadsFromMap() | Session info
Package: nucleoSim 1.41.0
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_1.41.0.tar.gz
nucleoSim_1.41.0.zip(r-4.7-any)nucleoSim_1.41.0.zip(r-4.6-any)nucleoSim_1.41.0.zip(r-4.5-any)
nucleoSim_1.41.0.tgz(r-4.6-any)nucleoSim_1.41.0.tgz(r-4.5-any)
nucleoSim_1.41.0.tar.gz(r-4.7-any)nucleoSim_1.41.0.tar.gz(r-4.6-any)
nucleoSim_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nucleoSim/json (API)
| # 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-1.41.0(bioc 3.24)nucleoSim-1.40.0(bioc 3.23)
geneticssequencingsoftwarestatisticalmethodalignmentbioconductornucleosome-mapsnucleosomessimulationsimulatorsynthetic-nucleosomes
Last updated from:0d9bca7dc4. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 135 | ||
| linux-devel | NOTE | 179 | ||
| source / vignettes | OK | 183 | ||
| linux-release | NOTE | 210 | ||
| macos-release | NOTE | 96 | ||
| macos-oldrel | NOTE | 123 | ||
| windows-devel | NOTE | 93 | ||
| windows-release | NOTE | 94 | ||
| windows-oldrel | NOTE | 84 | ||
| wasm-release | OK | 95 |
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 |
