Package: NOISeq 2.51.0
Sonia Tarazona
NOISeq: Exploratory analysis and differential expression for RNA-seq data
Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions.
Authors:
NOISeq_2.51.0.tar.gz
NOISeq_2.51.0.zip(r-4.5)NOISeq_2.51.0.zip(r-4.4)NOISeq_2.51.0.zip(r-4.3)
NOISeq_2.51.0.tgz(r-4.4-any)NOISeq_2.51.0.tgz(r-4.3-any)
NOISeq_2.51.0.tar.gz(r-4.5-noble)NOISeq_2.51.0.tar.gz(r-4.4-noble)
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NOISeq.pdf |NOISeq.html✨
NOISeq/json (API)
NEWS
| # Install 'NOISeq' in R: |
| install.packages('NOISeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- mybiotypes - Marioni's dataset
- mychroms - Marioni's dataset
- mycounts - Marioni's dataset
- mydata - Example of objects used and created by the NOISeq package
- myfactors - Marioni's dataset
- mygc - Marioni's dataset
- mylength - Marioni's dataset
- mynoiseq - Example of objects used and created by the NOISeq package
On BioConductor:NOISeq-2.49.0(bioc 3.20)NOISeq-2.48.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyrnaseqdifferentialexpressionvisualizationsequencing
Last updated 23 days agofrom:bf39f9ca05. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | NOTE | Oct 30 2024 |
Exports:addDataARSyNseqdatdat2saveDE.plotdegenesexplo.plotfiltered.datanoiseqnoiseqbioPCA.GENESQCreportreadDatarpkmshowtmmuqua
Dependencies:BiobaseBiocGenericslatticeMatrix
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ASCA Removal of Systematic Noise on Seq data | ARSyNseq arsynseq |
| Biodetection class | Biodetection Biodetection-class dat2save,Biodetection-method explo.plot,Biodetection-method show,Biodetection-method |
| CD class | CD CD-class dat2save,CD-method explo.plot,CD-method show,CD-method |
| CountsBio class | CountsBio CountsBio-class dat2save,CountsBio-method explo.plot,CountsBio-method show,CountsBio-method |
| Exploration of expression data. | dat |
| Saving data generated for exploratory plots. | dat2save |
| Recovering differencially expressed features. | degenes |
| Plotting differential expression results | DE.plot |
| Example of objects used and created by the NOISeq package | mydata mynoiseq |
| Exploratory plots for expression data. | explo.plot |
| Methods to filter out low count features | filtered.data |
| GCbias class | dat2save,GCbias-method explo.plot,GCbias-method GCbias GCbias-class show,GCbias-method |
| lengthbias class | dat2save,lengthbias-method explo.plot,lengthbias-method lengthbias lengthbias-class show,lengthbias-method |
| Marioni's dataset | mybiotypes mychroms mycounts myfactors mygc mylength |
| Class myCounts | myCounts myCounts-class |
| Differential expression method for technical replicates or no replicates at all | noiseq |
| Differential expression method for biological replicates | noiseqbio |
| Normalization methods | rpkm tmm uqua |
| Output class of NOISeq | Output Output-class show,Output-method |
| PCA class | dat2save,PCA-method explo.plot,PCA-method PCA PCA-class show,PCA-method |
| Principal Component Analysis | PCA.GENES |
| Quality Control report for expression data | QCreport |
| Creating an object of eSet class | addData readData |
| Saturation class | dat2save,Saturation-method explo.plot,Saturation-method Saturation saturation Saturation-class show,Saturation-method |
