Package: scanMiR 1.19.0

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:Pierre-Luc Germain [cre, aut], Michael Soutschek [aut], Fridolin Gross [aut]

scanMiR_1.19.0.tar.gz
scanMiR_1.19.0.zip(r-4.7)scanMiR_1.19.0.zip(r-4.6)scanMiR_1.19.0.zip(r-4.5)
scanMiR_1.19.0.tgz(r-4.6-any)scanMiR_1.19.0.tgz(r-4.5-any)
scanMiR_1.19.0.tar.gz(r-4.7-any)scanMiR_1.19.0.tar.gz(r-4.6-any)
scanMiR_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scanMiR/json (API)

# Install 'scanMiR' in R:
install.packages('scanMiR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:scanMiR-1.19.0(bioc 3.24)scanMiR-1.18.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

mirnasequencematchingalignment

5.78 score 1 packages 67 scripts 18 exports 39 dependencies

Last updated from:a482f71c94. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING181
linux-devel-x86_64NOTE240
source / vignettesOK222
linux-release-x86_64NOTE290
macos-release-arm64NOTE130
macos-oldrel-arm64NOTE132
windows-develNOTE195
windows-releaseNOTE178
windows-oldrelNOTE167
wasm-releaseOK135

Exports:aggregateMatchesassignKdTypeconservationdummyKdDatafindSeedMatchesget3pAlignmentget8merRangegetKdModelgetKmersgetMatchTypesgetRandomSeqgetSeed8mersKdModelListplotKdModelremoveOverlappingRangesshowsummaryviewTargetAlignment

Dependencies:BHBiocGenericsBiocParallelBiostringsclicodetoolscowplotcpp11crayondata.tablefarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableIRangesisobandlabelinglambda.rlifecyclepwalignR6RColorBrewerrlangS4VectorsS7scalesSeqinfoseqLogosnowstringivctrsviridisLitewithrXVector

miRNA affinity models and the KdModel class
12-mer dissociation rates | KdModels | KdModelLists | Creating a KdModel object | Common KdModel collections | Under the hood | Session info
Rendered fromKdmodels.Rmdusingknitr::rmarkdown

Last update: 2024-04-15
Started: 2021-04-13

Scanning sequences for miRNA binding sites and exploring matches with scanMiR
Scanning | Background | Basic Scan | Using a miRNA Seed | Using a miRNA sequence | Using a KdModel | About match types | Further Options | ORF length | Supplementary 3' pairing | Shadow and Overlapping Matches | Aggregation on the fly | Aggregating Sites | Basic Aggregation | Dealing with very large scans | Multithreading | Dealing with large collections of predictions | Session info
Rendered fromscanning.Rmdusingknitr::rmarkdown

Last update: 2023-06-08
Started: 2021-04-13

Readme and manuals

Help Manual

Help pageTopics
aggregateMatchesaggregateMatches
assignKdTypeassignKdType
conservationconservation
Create dummy log_kd per 12-mer datadummyKdData
Predicting and characterizing miRNA binding sitesfindSeedMatches
Finds 3' complementary binding of a miRNAget3pAlignment
get8merRangeget8merRange
getKdModelgetKdModel
getKmersgetKmers
getMatchTypesgetMatchTypes
getRandomSeqgetRandomSeq
getSeed8mersgetSeed8mers
miRNA affinity modelsc,KdModel-method KdModel KdModel-class KdModel-methods show,KdModel-method summary,KdModel-method
KdModelListKdModelList KdModelList-class
Methods for the 'KdModelList' classesKdModelList-methods KdModelList-methods,KdModelList-method summary,KdModelList-method [,KdModelList,ANY-method [,KdModelList-methods,KdModelList-method
plotKdModelplotKdModel
removeOverlappingRangesremoveOverlappingRanges
Example KdModel (hsa-miR-155-5p)SampleKdModel
Example transcript sequenceSampleTranscript
viewTargetAlignmentviewTargetAlignment