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-4.5)denoiSeq_0.1.1.zip(r-4.4)denoiSeq_0.1.1.zip(r-4.3)
denoiSeq_0.1.1.tgz(r-4.4-any)denoiSeq_0.1.1.tgz(r-4.3-any)
denoiSeq_0.1.1.tar.gz(r-4.5-noble)denoiSeq_0.1.1.tar.gz(r-4.4-noble)
denoiSeq_0.1.1.tgz(r-4.4-emscripten)denoiSeq_0.1.1.tgz(r-4.3-emscripten)
denoiSeq.pdf |denoiSeq.html✨
denoiSeq/json (API)
NEWS
| # 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 7 years agofrom:96e6299657. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 09 2024 |
| R-4.5-win | WARNING | Oct 09 2024 |
| R-4.5-linux | WARNING | Oct 09 2024 |
| R-4.4-win | WARNING | Oct 09 2024 |
| R-4.4-mac | WARNING | Oct 09 2024 |
| R-4.3-win | WARNING | Oct 09 2024 |
| R-4.3-mac | WARNING | Oct 09 2024 |
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 |
