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