Introduction | Raw and annotation data | Raw data normalization | Troubleshooting and fine-tuning options | Concrete example with provided data | Content of the file ''samplesinfo.txt''
Package: ExiMiR 2.55.0
Sylvain Gubian
ExiMiR: R functions for the normalization of Exiqon miRNA array data
This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.
Authors:
ExiMiR_2.55.0.tar.gz
ExiMiR_2.55.0.zip(r-4.7)ExiMiR_2.55.0.zip(r-4.6)ExiMiR_2.55.0.zip(r-4.5)
ExiMiR_2.55.0.tgz(r-4.6-any)ExiMiR_2.55.0.tgz(r-4.5-any)
ExiMiR_2.55.0.tar.gz(r-4.7-any)ExiMiR_2.55.0.tar.gz(r-4.6-any)
ExiMiR_2.55.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ExiMiR/json (API)
| # Install 'ExiMiR' in R: |
| install.packages('ExiMiR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
On BioConductor:ExiMiR-2.55.0(bioc 3.24)ExiMiR-2.54.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarrayonechanneltwochannelpreprocessinggeneexpressiontranscription
Last updated from:271382b0d3. Checks:1 FAILURE, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | FAILURE | 184 | ||
| linux-devel-x86_64 | NOTE | 202 | ||
| source / vignettes | OK | 260 | ||
| linux-release-x86_64 | NOTE | 207 | ||
| macos-release-arm64 | NOTE | 121 | ||
| macos-oldrel-arm64 | NOTE | 91 | ||
| windows-devel | NOTE | 499 | ||
| windows-release | NOTE | 492 | ||
| windows-oldrel | NOTE | 486 | ||
| wasm-release | OK | 111 |
Exports:bg.correct.miRcreateABmake.gal.envnorm.miRNormiRNormiR.bgcorrect.methodsNormiR.normalize.methodsNormiR.pmcorrect.methodsNormiR.spikein.argsNormiR.summary.methodsReadExisummarize.miR
Dependencies:affyaffyioBiobaseBiocGenericsBiocManagergenericslimmapreprocessCorestatmod
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| R functions for the normalization of Exiqon miRNA array data | ExiMiR |
| ExiMiR low-level function for background correction | bg.correct.miR |
| ExiMiR function for creating an AffyBatch object from other object types (RGList, EListRaw, MAList or list) | createAB |
| R annotation environment for GEO series GSE20122 | galenv |
| Affybatch object for the raw data from GEO series GSE19183 | GSE19183 |
| Affybatch object for the raw data from GEO series GSE20122 | GSE20122 |
| GAL Environment Maker | make.gal.env |
| ExiMiR low-level function for miRNA raw data normalization. | norm.miR |
| ExiMiR high-level function for miRNA raw data normalization. | NormiR |
| ExiMiR functions for enumerating the names of low-level normalization methods or arguments | NormiR.bgcorrect.methods NormiR.normalize.methods NormiR.pmcorrect.methods NormiR.spikein.args NormiR.summary.methods |
| ExiMiR function for reading Exiqon raw data into an AffyBatch object. | ReadExi |
| ExiMiR low-level function for summarization. | summarize.miR |