Overview | Introduction | Background | Reference | Workflow Integration | Sample Data | RBNS Data | eCLIP Data | Setup | In Vitro Specificity from Pre-computed Enrichment Data (RBNS) | Loading RBNS Data | Calculating Specificity and Sensitivity for All Four RBPs | Visualization | Specificity Distribution Plots | Sensitivity Profile Plots | Cellular Specificity from De Novo Enrichment (eCLIP) | Loading Peak Data | Running motifEnrichment Pipeline | Comparing In Vitro (RBNS) vs. Cellular (eCLIP) Specificity | Session Info
Package: RBPSpecificity 0.99.6
Soon Yi
RBPSpecificity: RBP Inherent Specificity and Variation Sensitivity Analysis Tool
Provides tools to analyze RNA Binding Protein (RBP) binding specificities from high-throughput sequencing data. Functions include calculating K-mer enrichment, Inherent Specificity (IS), and Mutational Sensitivity (VS), along with visualization of IS and VS. For detailed methodology and applications, please refer to our manuscript (see URL field or vignette).
Authors:
RBPSpecificity_0.99.6.tar.gz
RBPSpecificity_0.99.6.zip(r-4.7)RBPSpecificity_0.99.6.zip(r-4.6)RBPSpecificity_0.99.6.zip(r-4.5)
RBPSpecificity_0.99.6.tgz(r-4.6-any)RBPSpecificity_0.99.6.tgz(r-4.5-any)
RBPSpecificity_0.99.6.tar.gz(r-4.7-any)RBPSpecificity_0.99.6.tar.gz(r-4.6-any)
RBPSpecificity_0.99.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RBPSpecificity/json (API)
| # Install 'RBPSpecificity' in R: |
| install.packages('RBPSpecificity', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/s00nyi/rbpspecificity/issues
softwaremotifannotationsequencingcoveragegenomeannotationvisualizationgeneregulationkegg
Last updated from:e1b8712b78. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 270 | ||
| linux-devel-x86_64 | OK | 602 | ||
| source / vignettes | OK | 395 | ||
| linux-release-x86_64 | OK | 594 | ||
| macos-release-arm64 | OK | 473 | ||
| macos-oldrel-arm64 | OK | 487 | ||
| windows-devel | OK | 501 | ||
| windows-release | OK | 505 | ||
| windows-oldrel | OK | 499 | ||
| wasm-release | OK | 225 |
Exports:motifEnrichmentplotSensitivityplotSpecificityreturnSensitivityreturnSpecificity
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecigarilloclicodetoolscpp11crayoncurlDelayedArrayfarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslplyrR6RColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsviridisLitewithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| RBPSpecificity: Analyze RBP Binding Specificity and Variation Sensitivity | RBPSpecificity-package RBPSpecificity |
| Calculate K-mer Motif Enrichment from Genomic Coordinates | motifEnrichment |
| Plot Sensitivity Matrix | plotSensitivity |
| Plot Specificity Distribution | plotSpecificity |
| Calculate Sensitivity | returnSensitivity |
| Calculate Specificity | returnSpecificity |
