Installation | Introduction | Data input | Differential expression analysis | Pulling out DE results | Visualization | Session info | References
Package: NBAMSeq 1.29.0
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_1.29.0.tar.gz
NBAMSeq_1.29.0.zip(r-4.7)NBAMSeq_1.29.0.zip(r-4.6)NBAMSeq_1.29.0.zip(r-4.5)
NBAMSeq_1.29.0.tgz(r-4.6-any)NBAMSeq_1.29.0.tgz(r-4.5-any)
NBAMSeq_1.29.0.tar.gz(r-4.7-any)NBAMSeq_1.29.0.tar.gz(r-4.6-any)
NBAMSeq_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
NBAMSeq/json (API)
| # 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-1.29.0(bioc 3.24)NBAMSeq-1.28.0(bioc 3.23)
rnaseqdifferentialexpressiongeneexpressionsequencingcoveragedifferential-expressiongene-expressiongeneralized-additive-modelsgeneralized-linear-modelsnegative-binomial-regressionsplines
Last updated from:5c0fbc2d31. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 193 | ||
| linux-devel-x86_64 | NOTE | 334 | ||
| source / vignettes | OK | 269 | ||
| linux-release-x86_64 | NOTE | 372 | ||
| macos-release-arm64 | NOTE | 197 | ||
| macos-oldrel-arm64 | NOTE | 150 | ||
| windows-devel | NOTE | 254 | ||
| windows-release | NOTE | 269 | ||
| windows-oldrel | NOTE | 257 | ||
| wasm-release | OK | 179 |
Exports:getDesigngetsfmakeExamplemakeplotNBAMSeqNBAMSeqDataSetresultssetsf<-
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayDESeq2farverfastmapformatRfutile.loggerfutile.optionsgenefiltergenericsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpkgconfigpngR6RColorBrewerRcppRcppArmadillorlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimentsurvivalsysvctrsviridisLitewithrXMLxtableXVector
NBAMSeq: Negative Binomial Additive Model for RNA-Seq Data
Last update: 2020-02-18
Started: 2019-04-03
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 |
