Bioconductor Bindingsitefinder
Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to...
Install
npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-bindingsitefinder -g -a claude-code -y- Repository
- bioMate-AI/biomate-bioconductor-kb793
- Category
- Engineering
- Updated
- 5mo ago
- License
- See repository
- Context cost
- Lightabout 1,348 tokens
- Runs scripts
- No, instructions only
What it does
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.
BindingSiteFinder
Workflows
Standard Workflow
library(BindingSiteFinder)
library(txdbmaker)
library(rtracklayer)
# 1. Import crosslink sites
csFile <- system.file("extdata", "PureCLIP_crosslink_sites_examples.bed", package="BindingSiteFinder")
cs <- rtracklayer::import(con = csFile, format = "BED")
# 2. Create metadata table and construct BSFDataSet
files <- system.file("extdata", package="BindingSiteFinder")
clipFilesP <- list.files(files, pattern = "plus.bw$", full.names = TRUE)
clipFilesM <- list.files(files, pattern = "minus.bw$", full.names = TRUE)
meta <- data.frame(
id = 1:4,
condition = factor(rep("WT", 4)),
clPlus = clipFilesP,
clMinus = clipFilesM
)
bds <- BSFDataSetFromBigWig(ranges = cs, meta = meta, silent = TRUE)
# 3. Build gene and transcript region annotations
annoDb <- txdbmaker::makeTxDbFromGFF(file = "gencode_v37_annotation.gff3", format = "gff3")
gns <- genes(annoDb)
regions <- GRangesList(
CDS = cds(annoDb),
Intron = unlist(intronsByTranscript(annoDb)),
UTR3 = unlist(threeUTRsByTranscript(annoDb)),
UTR5 = unlist(fiveUTRsByTranscript(annoDb))
)
# 4. Run BSFind wrapper
bdsOut <- BSFind(
object = bds,
anno.genes = gns,
anno.transcriptRegionList = regions,
est.subsetChromosome = "chr22",
veryQuiet = TRUE
)
# 5. Export results
exportToBED(bdsOut, con = "./myBindingSites.bed")
Input/Output Note: Inputs a BSFDataSet and genomic annotations; outputs a refined BSFDataSet with defined binding sites and exports them to a BED file.
Differential Binding Analysis
library(BindingSiteFinder)
library(txdbmaker)
# 1. Load Gene Annotations and Transcript Regions
annoDb <- txdbmaker::makeTxDbFromGFF(file = "gencode_v37_annotation.gff3", format = "gff3")
gns <- genes(annoDb)
regions <- GRangesList(
CDS = cds(annoDb),
Intron = unlist(intronsByTranscript(annoDb)),
UTR3 = unlist(threeUTRsByTranscript(annoDb)),
UTR5 = unlist(fiveUTRsByTranscript(annoDb))
)
