Package: eisaR 1.19.0
Michael Stadler
eisaR: Exon-Intron Split Analysis (EISA) in R
Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.
Authors:
eisaR_1.19.0.tar.gz
eisaR_1.19.0.zip(r-4.5)eisaR_1.19.0.zip(r-4.4)eisaR_1.19.0.zip(r-4.3)
eisaR_1.19.0.tgz(r-4.4-any)eisaR_1.19.0.tgz(r-4.3-any)
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eisaR.pdf |eisaR.html✨
eisaR/json (API)
NEWS
| # Install 'eisaR' in R: |
| install.packages('eisaR', repos = c('https://fmicompbio.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fmicompbio/eisar/issues
On BioConductor:eisaR-1.17.1(bioc 3.20)eisaR-1.16.0(bioc 3.19)
transcriptiongeneexpressiongeneregulationfunctionalgenomicstranscriptomicsregressionrnaseq
Last updated 23 days agofrom:d8c11e00b4. Checks:OK: 1 ERROR: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 29 2024 |
| R-4.5-win | ERROR | Oct 30 2024 |
| R-4.5-linux | ERROR | Oct 30 2024 |
| R-4.4-win | ERROR | Oct 30 2024 |
| R-4.4-mac | ERROR | Oct 30 2024 |
| R-4.3-win | ERROR | Oct 30 2024 |
| R-4.3-mac | ERROR | Oct 30 2024 |
Exports:exportToGtfgetFeatureRangesgetRegionsFromTxDbgetTx2GeneplotEISArunEISA
Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArrayedgeRGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticelimmalocfitMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraystatmodSummarizedExperimentsysUCSC.utilsXVectorzlibbioc
Generating reference files for spliced and unspliced abundance estimation with alignment-free methods
Rendered fromrna-velocity.Rmdusingknitr::rmarkdownon Oct 29 2024.Last update: 2020-03-28
Started: 2020-03-12
Using eisaR for Exon-Intron Split Analysis (EISA)
Rendered fromeisaR.Rmdusingknitr::rmarkdownon Oct 29 2024.Last update: 2024-03-14
Started: 2018-11-29
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Export GRangesList to GTF | exportToGtf |
| Generate a GRangesList object with feature ranges | getFeatureRanges |
| Get exonic/gene body regions from a transcript database. | getRegionsFromTxDb |
| Generate a transcript-to-gene mapping from a GRangesList | getTx2Gene |
| Visualize the results from an exon-intron split analysis. | plotEISA |
| Run Exon-Intron Split Analysis. | runEISA |
