Diagnostics
Package: denoiSeq 0.1.1
denoiSeq: Differential Expression Analysis Using a Bottom-Up Model
Given count data from two conditions, it determines which transcripts are differentially expressed across the two conditions using Bayesian inference of the parameters of a bottom-up model for PCR amplification. This model is developed in Ndifon Wilfred, Hilah Gal, Eric Shifrut, Rina Aharoni, Nissan Yissachar, Nir Waysbort, Shlomit Reich Zeliger, Ruth Arnon, and Nir Friedman (2012), <http://www.pnas.org/content/109/39/15865.full>, and results in a distribution for the counts that is a superposition of the binomial and negative binomial distribution.
Authors:
denoiSeq_0.1.1.tar.gz
denoiSeq_0.1.1.zip(r-4.7-any)denoiSeq_0.1.1.zip(r-4.6-any)denoiSeq_0.1.1.zip(r-4.5-any)
denoiSeq_0.1.1.tgz(r-4.6-any)denoiSeq_0.1.1.tgz(r-4.5-any)
denoiSeq_0.1.1.tar.gz(r-4.7-any)denoiSeq_0.1.1.tar.gz(r-4.6-any)
denoiSeq_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
denoiSeq/json (API)
| # Install 'denoiSeq' in R: |
| install.packages('denoiSeq', repos = c('https://buriom.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/buriom/denoiseq/issues
Last updated from:96e6299657. Checks:7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | WARNING | 146 | ||
| source / vignettes | OK | 251 | ||
| linux-release | WARNING | 139 | ||
| macos-release | WARNING | 173 | ||
| macos-oldrel | WARNING | 206 | ||
| windows-devel | WARNING | 92 | ||
| windows-release | WARNING | 68 | ||
| windows-oldrel | WARNING | 80 | ||
| wasm-release | OK | 113 |
Exports:denoiseqgetSamplesOfresultssetInitValuessetReplicatessetStepSizestunedStepSize
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Differential expression analysis using a bottom-up model | denoiseq |
| ERCC dataset | ERCC |
| Get posterior samples of a parameter | getSamplesOf |
| An S4 class to represent summarised counts and the output of Bayesian inference. | readsData |
| Compute the test statistic | results |
| Generic for altering the initValues slot | setInitValues setInitValues,readsData-method |
| Mutator method for the output slot of the readsData object. | setOutput,readsData-method |
| Generic for the altering setReplicates slot. | setReplicates setReplicates,readsData-method |
| Mutator method for the replicates slot of the readsData object. | setReplicates,readsData-method |
| Generic for altering the stepSizes slot. | setStepSizes setStepSizes,readsData-method |
| Mutator method for the stepSizes slot of the readsData object. | setStepSizes,readsData-method |
| simulated data | simdat |
| Get values of the tuned step sizes. | tunedStepSize |