1 Main changes in the DRIMSeq package | 2 Overview of the Dirichlet-multinomial model | 3 Important notes | 4 Hints for DRIMSeq pipelines | 5 Differential transcript usage analysis workflow | 6 tuQTL analysis workflow | 7 Session information
Package: DRIMSeq 1.41.0
Malgorzata Nowicka
DRIMSeq: Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.
Authors:
DRIMSeq_1.41.0.tar.gz
DRIMSeq_1.41.0.zip(r-4.7)DRIMSeq_1.41.0.zip(r-4.6)DRIMSeq_1.41.0.zip(r-4.5)
DRIMSeq_1.41.0.tgz(r-4.6-any)DRIMSeq_1.41.0.tgz(r-4.5-any)
DRIMSeq_1.41.0.tar.gz(r-4.7-any)DRIMSeq_1.41.0.tar.gz(r-4.6-any)
DRIMSeq_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DRIMSeq/json (API)
| # Install 'DRIMSeq' in R: |
| install.packages('DRIMSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:DRIMSeq-1.41.0(bioc 3.24)DRIMSeq-1.40.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysnpalternativesplicingdifferentialsplicinggeneticsrnaseqsequencingworkflowstepmultiplecomparisongeneexpressiondifferentialexpression
Last updated from:47ade4497c. Checks:8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 172 | ||
| linux-devel-x86_64 | WARNING | 353 | ||
| source / vignettes | OK | 324 | ||
| linux-release-x86_64 | WARNING | 349 | ||
| macos-release-arm64 | WARNING | 154 | ||
| macos-oldrel-arm64 | WARNING | 142 | ||
| windows-devel | WARNING | 241 | ||
| windows-release | WARNING | 252 | ||
| windows-oldrel | WARNING | 246 | ||
| wasm-release | OK | 176 |
Exports:coefficientscolnamescolnames<-common_precisioncommon_precision<-countsdesigndmDSdatadmFilterdmFitdmPrecisiondmSQTLdatadmTestelementNROWSgenewise_precisiongenewise_precision<-mean_expressionncolnrowplotDataplotPrecisionplotProportionsplotPValuesproportionsresultsrownamesrownames<-samples
Dependencies:BHBiocGenericsBiocParallelclicodetoolscpp11edgeRfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSplyrR6RColorBrewerRcppreshape2rlangS4VectorsS7scalesSeqinfosnowstatmodstringistringrvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot the frequency of present features | dm_plotDataDSInfo |
| Plot feature proportions | dm_plotProportions |
| Create dmDSdata object | dmDSdata |
| dmDSdata object | counts,dmDSdata-method dmDSdata-class length,dmDSdata-method names,dmDSdata-method samples samples,dmDSdata-method [,dmDSdata,ANY-method [,dmDSdata-method |
| dmDSfit object | coefficients,dmDSfit-method design,dmDSfit-method dmDSfit-class proportions proportions,dmDSfit-method |
| dmDSprecision object | common_precision common_precision,dmDSprecision-method common_precision<- common_precision<-,dmDSprecision-method design,dmDSprecision-method dmDSprecision-class genewise_precision genewise_precision,dmDSprecision-method genewise_precision<- genewise_precision<-,dmDSprecision-method mean_expression mean_expression,dmDSprecision-method |
| dmDStest object | design,dmDStest-method dmDStest-class results results,dmDStest-method |
| Filtering | dmFilter dmFilter,dmDSdata-method dmFilter,dmSQTLdata-method |
| Fit the Dirichlet-multinomial and/or the beta-binomial full model regression | dmFit dmFit,dmDSprecision-method dmFit,dmSQTLprecision-method |
| Estimate the precision parameter in the Dirichlet-multinomial model | dmPrecision dmPrecision,dmDSdata-method dmPrecision,dmSQTLdata-method |
| Create dmSQTLdata object | dmSQTLdata |
| dmSQTLdata object | counts,dmSQTLdata-method dmSQTLdata-class length,dmSQTLdata-method names,dmSQTLdata-method samples,dmSQTLdata-method [,dmSQTLdata,ANY-method [,dmSQTLdata-method |
| dmSQTLfit object | dmSQTLfit-class |
| dmSQTLprecision object | common_precision,dmSQTLprecision-method dmSQTLprecision-class genewise_precision,dmSQTLprecision-method mean_expression,dmSQTLprecision-method |
| dmSQTLtest object | dmSQTLtest-class results,dmSQTLtest-method |
| Likelihood ratio test to detect differential transcript/exon usage | dmTest dmTest,dmDSfit-method dmTest,dmSQTLfit-method |
| MatrixList object | $,MatrixList-method colnames,MatrixList-method colnames<-,MatrixList-method dim,MatrixList-method elementNROWS,MatrixList-method length,MatrixList-method MatrixList-class names,MatrixList-method names<-,MatrixList-method ncol,MatrixList-method nrow,MatrixList-method rownames,MatrixList-method rownames<-,MatrixList-method [,MatrixList,ANY-method [,MatrixList-method [[,MatrixList-method |
| Plot data summary | plotData plotData,dmDSdata-method plotData,dmSQTLdata-method |
| Precision versus mean expression plot | plotPrecision plotPrecision,dmDSprecision-method plotPrecision,dmSQTLprecision-method |
| Plot feature proportions | plotProportions plotProportions,dmDSfit-method plotProportions,dmSQTLfit-method |
| Plot p-value distribution | plotPValues plotPValues,dmDStest-method plotPValues,dmSQTLtest-method |
