Last data update: 2014.03.03
Data Source
Data Type
Classification
Cran Task View
BiocViews
SMO (statistical methods ontology)
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Convert BED format to RangedData. This function will be depreciated.
● Data Source:
BioConductor
These functions are provided for compatibility with older versions of R only, and may be defunct as soon as the next release.
● Data Source:
BioConductor
The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites leveraging biomaRt, IRanges, Biostrings, BSgenome, GO.db, hypergeometric test phyper and multtest package.
● Data Source:
BioConductor
Convert GFF format to RangedData. This function will be depreciated. Use function toGRanges instead.
● Data Source:
BioConductor
Using IDR to assess the consistency of replicate experiments and obtain a high-confidence single set of peaks
● Data Source:
BioConductor
Add GO IDs of the ancestors for a given vector of GO IDs leveraging GO.db package
● Data Source:
BioConductor
Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq id leveraging organism annotation dataset. For example, org.Hs.eg.db is the dataset from orgs.Hs.eg.db package for human, while org.Mm.eg.db is the dataset from the org.Mm.eg.db package for mouse
● Data Source:
BioConductor
Add metadata to to overlapping peaks after calling findOverlapsOfPeaks.
● Data Source:
BioConductor
An object of class annoGR represents the annotation data could be used by annotationPeakInBatch.
● Data Source:
BioConductor
Annotate peaks by annoGR object in the given range.
● Data Source:
BioConductor
providing 
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