Package: NBAMSeq 1.23.0

Xu Ren

NBAMSeq: Negative Binomial Additive Model for RNA-Seq Data

High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. NBAMSeq a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation.

Authors:Xu Ren [aut, cre], Pei Fen Kuan [aut]

NBAMSeq_1.23.0.tar.gz
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NBAMSeq.pdf |NBAMSeq.html
NBAMSeq/json (API)
NEWS

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

Bug tracker:https://github.com/reese3928/nbamseq/issues

On BioConductor:NBAMSeq-1.23.0(bioc 3.21)NBAMSeq-1.22.0(bioc 3.20)

rnaseqdifferentialexpressiongeneexpressionsequencingcoveragedifferential-expressiongene-expressiongeneralized-additive-modelsgeneralized-linear-modelsnegative-binomial-regressionsplines

4.78 score 2 stars 2 scripts 348 downloads 3 mentions 8 exports 84 dependencies

Last updated 5 months agofrom:fbb8e45362. Checks:6 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-winNOTEMar 29 2025
R-4.5-macNOTEMar 29 2025
R-4.5-linuxNOTEMar 29 2025
R-4.4-winOKMar 29 2025
R-4.4-macOKMar 29 2025
R-4.4-linuxOKMar 29 2025
R-4.3-winOKMar 29 2025
R-4.3-macOKMar 29 2025

Exports:getDesigngetsfmakeExamplemakeplotNBAMSeqNBAMSeqDataSetresultssetsf<-

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDESeq2fansifarverfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerRcppRcppArmadillorlangRSQLiteS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsurvivalsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVector

NBAMSeq: Negative Binomial Additive Model for RNA-Seq Data

Rendered fromNBAMSeq-vignette.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2020-02-18
Started: 2019-04-03

Readme and manuals

Help Manual

Help pageTopics
Make an example NBAMSeqDataSetmakeExample
Making plots to visualize nonlinear associationsmakeplot
Differential expression analysis based on negative binomial additive modelNBAMSeq
Accessor functions and replace methods for NBAMSeqDataSet objectgetDesign getDesign,NBAMSeqDataSet-method getsf getsf,NBAMSeqDataSet-method NBAMSeq-methods setsf<- setsf<-,NBAMSeqDataSet,numeric-method
NBAMSeqDataSet constructorNBAMSeqDataSet
NBAMSeqDataSet classNBAMSeqDataSet-class
Pulling out resultresults