doi:10.1186/s12859-020-3450-9> for details on the implemented methods.">

seqgendiff: RNA-Seq Generation/Modification for Simulation (original) (raw)

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 (2020) <doi:10.1186/s12859-020-3450-9> for details on the implemented methods.

Version: 1.2.4
Imports: assertthat, irlba, sva, pdist, matchingR, clue
Suggests: covr, testthat (≥ 2.1.0), SummarizedExperiment, DESeq2, knitr, rmarkdown, airway, limma, qvalue, edgeR
Published: 2024-05-15
DOI: 10.32614/CRAN.package.seqgendiff
Author: David Gerard ORCID iD [aut, cre]
Maintainer: David Gerard <gerard.1787 at gmail.com>
BugReports: https://github.com/dcgerard/seqgendiff/issues
License: GPL-3
URL: https://github.com/dcgerard/seqgendiff
NeedsCompilation: no
Citation: seqgendiff citation info
Materials: README NEWS
In views: Omics
CRAN checks: seqgendiff results

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