Introduction | Statistical Methodology | 1. Hurdle Model | 2. Information Borrowing via Empirical Bayes | 3. Differential Expression Testing | Data Structure | Example Workflow | Interpreting Results | Multiple Testing Correction | Supported Input Format | Session Information
Package: LRDE 1.1.1
Ziyang Liu
LRDE: Differential Expression Analysis with Long Read RNA-Seq Data
Provides hurdle negative binomial models for differential expression analysis with long-read RNA-Seq data.
Authors:
LRDE_1.1.1.tar.gz
LRDE_1.1.1.zip(r-4.7)LRDE_1.1.1.zip(r-4.6)LRDE_1.1.1.zip(r-4.5)
LRDE_1.1.1.tgz(r-4.6-any)LRDE_1.1.1.tgz(r-4.5-any)
LRDE_1.1.1.tar.gz(r-4.7-any)LRDE_1.1.1.tar.gz(r-4.6-any)
LRDE_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
LRDE/json (API)
| # Install 'LRDE' in R: |
| install.packages('LRDE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ziyang773/lrde/issues
On BioConductor:LRDE-1.1.0(bioc 3.24)LRDE-0.99.6(bioc 3.23)
softwaredifferentialexpressionsequencingrnaseqlongreadgeneexpressionregression
Last updated from:e2383aa99c. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 213 | ||
| linux-devel-x86_64 | OK | 309 | ||
| source / vignettes | OK | 196 | ||
| linux-release-x86_64 | OK | 237 | ||
| macos-release-arm64 | OK | 210 | ||
| macos-oldrel-arm64 | OK | 148 | ||
| windows-devel | OK | 176 | ||
| windows-release | OK | 175 | ||
| windows-oldrel | OK | 174 | ||
| wasm-release | OK | 128 |
Exports:hurdle_LRT.disthurdle_LRT.meanhurdle_Wald_Test.disthurdle_Wald_Test.meanhurdle.LRThurdle.Wald.TestprepareDGEsizeFactorsEsttagwiseEst
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| LRDE: Differential Expression Analysis for Long-Read RNA-Seq Data | LRDE-package LRDE |
| Distributional Likelihood Ratio Test for Hurdle Negative Binomial Model | hurdle_LRT.dist |
| Mean-Based Likelihood Ratio Test for Hurdle Negative Binomial Model | hurdle_LRT.mean |
| Distributional Wald Test for Hurdle Negative Binomial Model | hurdle_Wald_Test.dist |
| Mean-Based Wald Test for Hurdle Negative Binomial Model | hurdle_Wald_Test.mean |
| Likelihood Ratio Test for Hurdle Negative Binomial Model | hurdle.LRT |
| Wald Test for Hurdle Negative Binomial Model | hurdle.Wald.Test |
| Prepare Count Data for Differential Expression Analysis | prepareDGE |
| Estimate Size Factors for Normalization | sizeFactorsEst |
| Tag-wise Dispersion Estimation for Hurdle Negative Binomial Model | tagwiseEst |
