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:
NBAMSeq_1.23.0.tar.gz
NBAMSeq_1.23.0.zip(r-4.5)NBAMSeq_1.23.0.zip(r-4.4)NBAMSeq_1.23.0.zip(r-4.3)
NBAMSeq_1.23.0.tgz(r-4.5-any)NBAMSeq_1.23.0.tgz(r-4.4-any)NBAMSeq_1.23.0.tgz(r-4.3-any)
NBAMSeq_1.23.0.tar.gz(r-4.5-noble)NBAMSeq_1.23.0.tar.gz(r-4.4-noble)
NBAMSeq_1.23.0.tgz(r-4.4-emscripten)NBAMSeq_1.23.0.tgz(r-4.3-emscripten)
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
Last updated 3 months agofrom:fbb8e45362. Checks:5 OK, 2 NOTE, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 28 2025 |
| R-4.5-win | NOTE | Jan 28 2025 |
| R-4.5-mac | WARNING | Jan 28 2025 |
| R-4.5-linux | NOTE | Jan 28 2025 |
| R-4.4-win | OK | Jan 28 2025 |
| R-4.4-mac | OK | Jan 28 2025 |
| R-4.3-win | OK | Jan 28 2025 |
| R-4.3-mac | OK | Jan 28 2025 |
Exports:getDesigngetsfmakeExamplemakeplotNBAMSeqNBAMSeqDataSetresultssetsf<-
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDESeq2fansifarverfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerRcppRcppArmadillorlangRSQLiteS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsurvivalsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Make an example NBAMSeqDataSet | makeExample |
| Making plots to visualize nonlinear associations | makeplot |
| Differential expression analysis based on negative binomial additive model | NBAMSeq |
| Accessor functions and replace methods for NBAMSeqDataSet object | getDesign getDesign,NBAMSeqDataSet-method getsf getsf,NBAMSeqDataSet-method NBAMSeq-methods setsf<- setsf<-,NBAMSeqDataSet,numeric-method |
| NBAMSeqDataSet constructor | NBAMSeqDataSet |
| NBAMSeqDataSet class | NBAMSeqDataSet-class |
| Pulling out result | results |
