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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NEWS

# Install 'seqgendiff' in R:
install.packages('seqgendiff', repos = c('https://dcgerard.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

On CRAN:

5.85 score 10 stars 71 scripts 199 downloads 1 mentions 13 exports 71 dependencies

Last updated 7 months agofrom:9629ad951b. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 14 2024
R-4.5-winOKDec 14 2024
R-4.5-linuxOKDec 14 2024
R-4.4-winNOTEDec 14 2024
R-4.4-macNOTEDec 14 2024
R-4.3-winNOTEDec 14 2024
R-4.3-macNOTEDec 14 2024

Exports:corassigneffective_corfix_corpoisthinselect_countsthin_2groupthin_allthin_basethin_diffthin_genethin_libThinDataToDESeqDataSetThinDataToSummarizedExperiment

Dependencies:annotateAnnotationDbiaskpassassertthatBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemcliclueclustercodetoolscpp11crayoncurlDBIedgeRfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesirlbajsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmatchingRMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpdistpkgconfigplogrpngR6RcppRcppArmadillorlangRSQLiteS4VectorssnowstatmodsurvivalsvasysUCSC.utilsvctrsXMLxtableXVectorzlibbioc

Applying Different Thinning Functions

Rendered fromdifferent_thinners.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2022-02-19
Started: 2019-07-17

Simulate RNA-seq Data from Real Data

Rendered fromsimulate_rnaseq.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2022-02-19
Started: 2019-05-23