Overview | Introduction | Background | Motivation | Mathematical Model | Reference | Installation | Setup | Data Loading | Loading RBP Models | Visualizing Raw Models | Setting Affinity Ranges | RNA-RBP Binding Simulations | Scenario 1: RBPs Binding to a Single RNA Target at Fixed Concentrations | Generating or Loading RNA Sequence | Running the Simulation | Visualization | Per-Position Binding Profile | Heatmap Visualization | Exporting Results | Scenario 2: RBP Binding with Varying Concentration Grid | Running Grid Simulation | Competition Grid Plot | Scenario 3: RBPs Binding to Multiple Target RNAs | Scenario 4: RBPs Binding to Multiple Target RNAs Across Different Concentrations | Session Info
Package: RBPEqBind 0.99.4
Soon Yi
RBPEqBind: RNA-Binding Protein Competitive Binding Simulation
Simulates competitive binding of N RBPs to RNA sequences using an equilibrium binding model. Supports single sequences, concentration grids, and transcriptome-wide analysis. Designed for Bioconductor.
Authors:
RBPEqBind_0.99.4.tar.gz
RBPEqBind_0.99.4.zip(r-4.7-any)RBPEqBind_0.99.4.zip(r-4.6-any)RBPEqBind_0.99.4.zip(r-4.5-any)
RBPEqBind_0.99.4.tgz(r-4.6-any)RBPEqBind_0.99.4.tgz(r-4.5-any)
RBPEqBind_0.99.4.tar.gz(r-4.7-any)RBPEqBind_0.99.4.tar.gz(r-4.6-any)
RBPEqBind_0.99.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RBPEqBind/json (API)
| # Install 'RBPEqBind' in R: |
| install.packages('RBPEqBind', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/s00nyi/rbpeqbind/issues
On BioConductor:RBPEqBind-0.99.4(bioc 3.24)
mathematicalbiologysystemsbiologyfunctionalgenomicstranscriptomicsgeneregulationvisualization
Last updated from:e1f34337a3. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 175 | ||
| linux-devel | OK | 399 | ||
| source / vignettes | OK | 472 | ||
| linux-release | OK | 309 | ||
| macos-release | OK | 243 | ||
| macos-oldrel | OK | 242 | ||
| windows-devel | OK | 271 | ||
| windows-release | OK | 240 | ||
| windows-oldrel | OK | 244 | ||
| wasm-release | OK | 128 |
Exports:callPeaksexportBedexportResultsgenerateRNAimportResultsloadModelmakeSEplotBindingplotGridplotHeatmapsetModelsimulateBindingsimulateBindingFastasimulateGridsimulateGridFastaviewModel
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurldata.tableDelayedArraydigestfarverformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicAlignmentsGenomicRangesggplot2globalsgluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelistenvMatrixMatrixGenericsmatrixStatsmimeopensslparallellyR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimentsysvctrsviridisLitewithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Call Peaks from Binding Simulation | callPeaks |
| Export BED format | exportBed |
| Export Results | exportResults |
| Generate Random RNA Sequence | generateRNA |
| Import Results | importResults |
| Load RBP Model from CSV | loadModel |
| Create SummarizedExperiment from Results | makeSE |
| Parse Genomic Coordinates from FASTA Header | parseGenomicHeader |
| Plot Binding Profile | plotBinding |
| Plot Competition Grid | plotGrid |
| Plot Binding Heatmap | plotHeatmap |
| Set Model Affinity (Score to Kd Conversion) | setModel |
| Simulate Competitive Binding | simulateBinding |
| Simulate Binding from FASTA File(s) | simulateBindingFasta |
| Simulate Concentration Grid | simulateGrid |
| Simulate Grid from FASTA File(s) | simulateGridFasta |
| View Model Affinity Distributions | viewModel |