seqgendiff: RNA-Seq Generation/Modification for Simulation

Generates/modifies RNA-seq data for use in simulations. We provide a suite of functions that will add a known amount of signal to a real RNA-seq dataset. The advantage of using this approach over simulating under a theoretical distribution is that common/annoying aspects of the data are more preserved, giving a more realistic evaluation of your method. The main functions are select_counts(), thin_diff(), thin_lib(), thin_gene(), thin_2group(), thin_all(), and effective_cor(). See Gerard (2019) <doi:10.1101/758524> for details on the implemented methods.

Version: 1.1.1
Imports: assertthat, irlba, sva, pdist, matchingR, clue, cate
Suggests: covr, testthat, SummarizedExperiment, DESeq2, knitr, rmarkdown, airway, limma, qvalue, edgeR, optmatch
Published: 2019-09-09
Author: David Gerard ORCID iD [aut, cre]
Maintainer: David Gerard <gerard.1787 at gmail.com>
BugReports: http://github.com/dcgerard/seqgendiff/issues
License: GPL-3
URL: https://github.com/dcgerard/seqgendiff
NeedsCompilation: no
Citation: seqgendiff citation info
Materials: README NEWS
CRAN checks: seqgendiff results

Downloads:

Reference manual: seqgendiff.pdf
Vignettes: Applying Different Thinning Functions
Simulate RNA-seq Data from Real Data
Package source: seqgendiff_1.1.1.tar.gz
Windows binaries: r-devel: seqgendiff_1.1.1.zip, r-release: seqgendiff_1.1.1.zip, r-oldrel: seqgendiff_1.1.1.zip
OS X binaries: r-release: seqgendiff_1.1.1.tgz, r-oldrel: seqgendiff_1.1.1.tgz
Old sources: seqgendiff archive

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