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 
[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.html , seqgendiff.pdf |
| Vignettes: |
Applying Different Thinning Functions (source, R code) Simulate RNA-seq Data from Real Data (source, R code) |
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:
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