Package: seqgendiff 1.2.4
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.
Authors:
seqgendiff_1.2.4.tar.gz
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seqgendiff.pdf |seqgendiff.html✨
seqgendiff/json (API)
NEWS
# Install 'seqgendiff' in R: |
install.packages('seqgendiff', repos = c('https://dcgerard.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dcgerard/seqgendiff/issues
Last updated 4 months agofrom:9629ad951b. Checks:OK: 2 NOTE: 5. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 16 2024 |
R-4.5-win | NOTE | Aug 16 2024 |
R-4.5-linux | OK | Aug 16 2024 |
R-4.4-win | NOTE | Aug 16 2024 |
R-4.4-mac | NOTE | Aug 16 2024 |
R-4.3-win | NOTE | Aug 16 2024 |
R-4.3-mac | NOTE | Aug 16 2024 |
Exports:corassigneffective_corfix_corpoisthinselect_countsthin_2groupthin_allthin_basethin_diffthin_genethin_libThinDataToDESeqDataSetThinDataToSummarizedExperiment
Dependencies:annotateAnnotationDbiaskpassassertthatBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemcliclueclustercodetoolscpp11crayoncurlDBIedgeRfastmapformatRfutile.loggerfutile.optionsgenefilterGenomeInfoDbGenomeInfoDbDatagluehttrIRangesirlbajsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmatchingRMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpdistpkgconfigplogrpngR6RcppRcppArmadillorlangRSQLiteS4VectorssnowstatmodsurvivalsvasysUCSC.utilsvctrsXMLxtableXVectorzlibbioc