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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 (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

Documentation:

Reference manual: seqgendiff.pdf
Vignettes: Applying Different Thinning Functions
Simulate RNA-seq Data from Real Data

Downloads:

Package source: seqgendiff_1.2.4.tar.gz
Windows binaries: r-devel: seqgendiff_1.2.4.zip, r-release: seqgendiff_1.2.4.zip, r-oldrel: seqgendiff_1.2.4.zip
macOS binaries: r-release (arm64): seqgendiff_1.2.4.tgz, r-oldrel (arm64): seqgendiff_1.2.4.tgz, r-release (x86_64): seqgendiff_1.2.4.tgz, r-oldrel (x86_64): seqgendiff_1.2.4.tgz
Old sources: seqgendiff archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=seqgendiff to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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