Package: scanMiR 1.13.0
Pierre-Luc Germain
scanMiR: scanMiR
A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
Authors:
scanMiR_1.13.0.tar.gz
scanMiR_1.13.0.zip(r-4.5)scanMiR_1.13.0.zip(r-4.4)scanMiR_1.13.0.zip(r-4.3)
scanMiR_1.13.0.tgz(r-4.4-any)scanMiR_1.13.0.tgz(r-4.3-any)
scanMiR_1.13.0.tar.gz(r-4.5-noble)scanMiR_1.13.0.tar.gz(r-4.4-noble)
scanMiR_1.13.0.tgz(r-4.4-emscripten)scanMiR_1.13.0.tgz(r-4.3-emscripten)
scanMiR.pdf |scanMiR.html✨
scanMiR/json (API)
NEWS
| # Install 'scanMiR' in R: |
| install.packages('scanMiR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- SampleKdModel - Example KdModel
- SampleTranscript - Example transcript sequence
On BioConductor:scanMiR-1.11.1(bioc 3.21)scanMiR-1.12.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
mirnasequencematchingalignment
Last updated 23 days agofrom:9306dd6f3e. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | WARNING | Oct 31 2024 |
Exports:aggregateMatchesassignKdTypeconservationdummyKdDatafindSeedMatchesget3pAlignmentget8merRangegetKdModelgetKmersgetMatchTypesgetRandomSeqgetSeed8mersKdModelListplotKdModelremoveOverlappingRangesshowsummaryviewTargetAlignment
Dependencies:askpassBHBiocGenericsBiocParallelBiostringsclicodetoolscolorspacecowplotcpp11crayoncurldata.tablefansifarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigpwalignR6RColorBrewerrlangS4VectorsscalesseqLogosnowstringisystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Scanning sequences for miRNA binding sites and exploring matches with scanMiR
Rendered fromscanning.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2023-06-08
Started: 2021-04-13
miRNA affinity models and the KdModel class
Rendered fromKdmodels.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2024-04-15
Started: 2021-04-13
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| aggregateMatches | aggregateMatches |
| assignKdType | assignKdType |
| conservation | conservation |
| Create dummy log_kd per 12-mer data | dummyKdData |
| Predicting and characterizing miRNA binding sites | findSeedMatches |
| Finds 3' complementary binding of a miRNA | get3pAlignment |
| get8merRange | get8merRange |
| getKdModel | getKdModel |
| getKmers | getKmers |
| getMatchTypes | getMatchTypes |
| getRandomSeq | getRandomSeq |
| getSeed8mers | getSeed8mers |
| miRNA affinity models | c,KdModel-method KdModel KdModel-class KdModel-methods show,KdModel-method summary,KdModel-method |
| KdModelList | KdModelList KdModelList-class |
| Methods for the 'KdModelList' classes | KdModelList-methods KdModelList-methods,KdModelList-method summary,KdModelList-method [,KdModelList,ANY-method [,KdModelList-methods,KdModelList-method |
| plotKdModel | plotKdModel |
| removeOverlappingRanges | removeOverlappingRanges |
| Example KdModel (hsa-miR-155-5p) | SampleKdModel |
| Example transcript sequence | SampleTranscript |
| viewTargetAlignment | viewTargetAlignment |
