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 user has choice between three different distributions for the read positioning: Normal, Student and Uniform.

Author
Rawane Samb [aut], Astrid DeschĂȘnes [cre, aut], Pascal Belleau [aut], Arnaud Droit [aut]
Date of publication
None
Maintainer
Astrid Deschenes <Astrid-Louise.Deschenes@crchudequebec.ulaval.ca>
License
Artistic-2.0
Version
1.2.0
URLs

View on Bioconductor

Man pages

createNucReadsFromNucMap
Create a synthetic nucleosome reads from a synthetic...
nucleoSim-package
nucleoSim: Generate synthetic nucleosome maps
plot.syntheticNucMap
Generate a graph of a synthetic nucleosome map
plot.syntheticNucReads
Generate a graph of a synthetic nucleosome map containing...
syntheticNucMapFromDist
Generate a synthetic nucleosome map containing complete...
syntheticNucMapFromDistValidation
Parameter validation for the 'syntheticNucMapFromDist'...
syntheticNucReadsFromDist
Generate a synthetic nucleosome map containing forward and...
syntheticNucReadsFromMap
Generate a synthetic nucleosome map containing forward and...
syntheticNucReadsValidation
Subsection of parameter validation for identical parameters...

Files in this package

nucleoSim/DESCRIPTION
nucleoSim/NAMESPACE
nucleoSim/NEWS
nucleoSim/R
nucleoSim/R/nucleoSim.R
nucleoSim/R/nucleoSimFunctions.R
nucleoSim/R/nucleoSimInternFunctions.R
nucleoSim/README.md
nucleoSim/build
nucleoSim/build/vignette.rds
nucleoSim/inst
nucleoSim/inst/doc
nucleoSim/inst/doc/nucleoSim.R
nucleoSim/inst/doc/nucleoSim.Rmd
nucleoSim/inst/doc/nucleoSim.html
nucleoSim/inst/unitTests
nucleoSim/inst/unitTests/Makefile.R
nucleoSim/inst/unitTests/test_syntheticNucMapFromDist.R
nucleoSim/inst/unitTests/test_syntheticNucReadsFromMap.R
nucleoSim/inst/unitTests/test_syntheticSampleFromDist.R
nucleoSim/man
nucleoSim/man/createNucReadsFromNucMap.Rd
nucleoSim/man/nucleoSim-package.Rd
nucleoSim/man/plot.syntheticNucMap.Rd
nucleoSim/man/plot.syntheticNucReads.Rd
nucleoSim/man/syntheticNucMapFromDist.Rd
nucleoSim/man/syntheticNucMapFromDistValidation.Rd
nucleoSim/man/syntheticNucReadsFromDist.Rd
nucleoSim/man/syntheticNucReadsFromMap.Rd
nucleoSim/man/syntheticNucReadsValidation.Rd
nucleoSim/tests
nucleoSim/tests/runTests.R
nucleoSim/vignettes
nucleoSim/vignettes/nucleoSim.Rmd