Package: BindingSiteFinder 2.5.2

Mirko Brüggemann

BindingSiteFinder: Binding site defintion based on iCLIP data

Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

Authors:Mirko Brüggemann [aut, cre], Melina Klostermann [aut], Kathi Zarnack [aut]

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BindingSiteFinder.pdf |BindingSiteFinder.html✨
BindingSiteFinder/json (API)
NEWS

# Install 'BindingSiteFinder' in R:

install.packages('BindingSiteFinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zarnackgroup/bindingsitefinder/issues

On BioConductor:BindingSiteFinder-2.5.2(bioc 3.21)BindingSiteFinder-2.4.0(bioc 3.20)

sequencing geneexpression generegulation functionalgenomics coverage dataimport binding-site-classification binding-sites bioconductor-package iclip rna-binding-proteins

5.65 score 6 stars 3 scripts 190 downloads 60 exports 134 dependencies

Last updated 3 months agofrom:d7f7545420. Checks:5 OK, 2 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 20 2025
R-4.5-win	NOTE	Jan 20 2025
R-4.5-linux	NOTE	Jan 20 2025
R-4.4-win	OK	Jan 20 2025
R-4.4-mac	OK	Jan 20 2025
R-4.3-win	OK	Jan 20 2025
R-4.3-mac	OK	Jan 20 2025

Exports:annotateWithScore assignToGenes assignToTranscriptRegions bindingSiteCoveragePlot bindingSiteDefinednessPlot BSFDataSet BSFDataSetFromBigWig BSFind calculateBsBackground calculateBsFoldChange calculateSignalToFlankScore clipCoverage collapseReplicates combineBSF coverageOverRanges duplicatedSitesPlot estimateBsWidth estimateBsWidthPlot exportTargetGenes exportToBED filterBsBackground geneOverlapsPlot getMeta getName getRanges getSignal getSummary globalScorePlot imputeBsDifferencesForTestdata makeBindingSites makeBsSummaryPlot mergeCrosslinkDiagnosticsPlot mergeSummaryPlot plotBsBackgroundFilter plotBsMA plotBsVolcano processingStepsFlowChart processingStepsTable pureClipGeneWiseFilter pureClipGlobalFilter pureClipGlobalFilterPlot quickFigure rangeCoveragePlot reproducibilityCutoffPlot reproducibilityFilter reproducibilityFilterPlot reproducibilitySamplesPlot reproducibilityScatterPlot setMeta setName setRanges setSignal setSummary show summary supportRatio supportRatioPlot targetGeneSpectrumPlot transcriptRegionOverlapsPlot transcriptRegionSpectrumPlot

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib cachem circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl DBI DelayedArray digest distributional doParallel dplyr evaluate fansi farver fastmap fontawesome forcats foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggdist ggforce ggplot2 GlobalOptions glue gtable highr htmltools httr IRanges isoband iterators jquerylib jsonlite kableExtra KEGGREST knitr labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme numDeriv openssl pillar pkgconfig plogr plyr png polyclip purrr quadprog R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales shape snow SparseArray stringi stringr SummarizedExperiment svglite sys systemfonts tibble tidyr tidyselect tinytex tweenr UCSC.utils utf8 vctrs viridisLite withr xfun XML xml2 XVector yaml

Definition of binding sites from iCLIP signal

Mirko Brüggemann, Kathi Zarnack

Rendered fromvignette.Rmdusingknitr::rmarkdownon Jan 20 2025.

Last update: 2024-11-20
Started: 2021-04-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add two 'BSFDataSet' objects	+,BSFDataSet,BSFDataSet-method add-BSFDataSet
Annotation function for BSFDataSet object	annotateWithScore
Assign binding sites to their hosting genes	assignToGenes
Assign binding sites to their hosting transcript regions	assignToTranscriptRegions
Plot signal coverage of selected ranges	bindingSiteCoveragePlot
Binding site definedness plot	bindingSiteDefinednessPlot
BSFDataSet object and constructors	BSFDataSet BSFDataSet, BSFDataSet-class, BSFDataSetFromBigWig
RBP binding site definition for iCLIP data	BSFind
Compute background coverage for binding sites per gene	calculateBsBackground
Compute fold-changes per binding site	calculateBsFoldChange
Calculate signal-to-flank score	calculateSignalToFlankScore
Coverage function for BSFDataSet objects	clipCoverage
Collapse signal from replicates	collapseReplicates
Combine multiple 'BSFDataSet' objects	combineBSF
Coverage function for BSFDataSet objects	coverageOverRanges
Plot the number of overlaps when assigning crosslink sites to genes	duplicatedSitesPlot
Function to estimate the appropriate binding site width together with the optimal gene-wise filter level.	estimateBsWidth
Plot the signal-to-flank score for varying gene-wise filter and binding site width	estimateBsWidthPlot
Function to export sorted RBP target genes	exportTargetGenes
Wrapper function to export binding sites as BED files	exportToBED
Filter for genes not suitable for differential testing	filterBsBackground
UpSet-plot to that shows the gene type overlaps	geneOverlapsPlot
Accessor method for the meta data of the BSFDataSet object	getMeta getMeta,BSFDataSet-method
Accessor method for the name of the BSFDataSet object	getName getName,BSFDataSet-method
Accessor method for the ranges of the BSFDataSet object	getRanges getRanges,BSFDataSet-method
Accessor method for the signal data of the BSFDataSet object	getSignal getSignal,BSFDataSet-method
Accessor method for the summary slot of the BSFDataSet object	getSummary getSummary,BSFDataSet-method
Plot the PureCLIP score distribution after re-assignment	globalScorePlot
Impute artificial differences in the example data set	imputeBsDifferencesForTestdata
Define equally sized binding sites from peak calling results and iCLIP crosslink events.	makeBindingSites
Plot binding site filter diagnostics	makeBsSummaryPlot
Plot binding site merging diagnostics	mergeCrosslinkDiagnosticsPlot
Plot summarized results of the different binding site merging and filtering steps	mergeSummaryPlot
Diagnostic plots for the differential binding background	plotBsBackgroundFilter
MA style plot	plotBsMA
Volcano style plot	plotBsVolcano
Step-wise flowchart plot	processingStepsFlowChart
Create a table of all workflow steps for reporting	processingStepsTable
Filter PureCLIP sites by their score distribution per gene	pureClipGeneWiseFilter
Filter PureCLIP sites by their score distribution	pureClipGlobalFilter
Plot the PureCLIP score distribution with global cutoff indicator	pureClipGlobalFilterPlot
Quick figures	quickFigure
Plot crosslink event coverage over binding site range	rangeCoveragePlot
Plot to that shows how many replicates support each binding site	reproducibilityCutoffPlot
Replicate reproducibility filter function	reproducibilityFilter
Plot to that shows the crosslink site distribution per replicate	reproducibilityFilterPlot
UpSet-plot to that shows how each replicate supports binding sites	reproducibilitySamplesPlot
Plot that shows binding site reproducibility as scatter	reproducibilityScatterPlot
Setter method for the meta data of the BSFDataSet object	setMeta setMeta,BSFDataSet-method
Setter method for the names of the BSFDataSet object The name slot holds the name information of the dataset	setName setName,BSFDataSet-method
Setter method for the ranges of the BSFDataSet object The GRanges object that holds the genomic ranges information can be replaced.	setRanges setRanges,BSFDataSet-method
Setter method for the signal data of the BSFDataSet object	setSignal setSignal,BSFDataSet-method
Setter method for the summary slot of the BSFDataSet object	setSummary setSummary,BSFDataSet-method
Show method to for the BSFDataSet	show show,BSFDataSet-method
Subset a BSFDataSet object	subset-BSFDataSet [,BSFDataSet,ANY,ANY,ANY-method
Summary method to for the BSFDataSet	summary summary,BSFDataSet-method
Support ratio function for BSFDataSet objects	supportRatio
Plot that shows the binding site support ratio	supportRatioPlot
Bar-chart to show the hosting gene types of binding sites	targetGeneSpectrumPlot
UpSet-plot to that shows the transcript region overlaps	transcriptRegionOverlapsPlot
Bar-chart to show the hosting transcript regions of binding sites	transcriptRegionSpectrumPlot