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:David Gerard [aut, cre]

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Bug tracker:https://github.com/dcgerard/seqgendiff/issues

On CRAN:

13 exports 9 stars 1.65 score 70 dependencies 1 mentions 56 scripts 282 downloads

Last updated 4 months agofrom:9629ad951b. Checks:OK: 2 NOTE: 5. Indexed: yes.

Exports:corassigneffective_corfix_corpoisthinselect_countsthin_2groupthin_allthin_basethin_diffthin_genethin_libThinDataToDESeqDataSetThinDataToSummarizedExperiment

Dependencies:annotateAnnotationDbiaskpassassertthatBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemcliclueclustercodetoolscpp11crayoncurlDBIedgeRfastmapformatRfutile.loggerfutile.optionsgenefilterGenomeInfoDbGenomeInfoDbDatagluehttrIRangesirlbajsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmatchingRMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpdistpkgconfigplogrpngR6RcppRcppArmadillorlangRSQLiteS4VectorssnowstatmodsurvivalsvasysUCSC.utilsvctrsXMLxtableXVectorzlibbioc