| Title: | Data supporting the SingleMoleculeFootprinting pkg |
|---|---|
| Description: | This Data package contains data objcets relevanat for the SingleMoleculeFootprinting package. More specifically, it contains one example of aligned sequencing data (.bam & .bai) necessary to run the SingleMoleculeFootprinting vignette. Additionally, we provide data that are essential for some functions to work correctly such as BaitCapture() and SampleCorrelation(). |
| Authors: | Guido Barzaghi [aut, cre] (ORCID: <https://orcid.org/0000-0001-6066-3920>), Arnaud Krebs [aut] (ORCID: <https://orcid.org/0000-0001-7999-6127>), Mike Smith [ctb] (ORCID: <https://orcid.org/0000-0002-7800-3848>) |
| Maintainer: | Guido Barzaghi <guido.barzaghi@embl.de> |
| License: | GPL-3 |
| Version: | 1.20.0 |
| Built: | 2026-10-10 11:14:33 UTC |
| Source: | https://github.com/bioc/SingleMoleculeFootprintingData |
This Data package contains r objcets necessary to run some of the functions from the SingleMoleculeFootprinting package. SingleMoleculeFootprinting is an R package providing functions to analyze Single Molecule Footprinting (SMF) data.
NRF1pair.bam(metadata = FALSE) NRF1pair.bam.bai(metadata = FALSE) EnrichmentRegions_mm10.rds(metadata = FALSE) ReferenceMethylation.rds(metadata = FALSE) AllCs.rds(metadata = FALSE)NRF1pair.bam(metadata = FALSE) NRF1pair.bam.bai(metadata = FALSE) EnrichmentRegions_mm10.rds(metadata = FALSE) ReferenceMethylation.rds(metadata = FALSE) AllCs.rds(metadata = FALSE)
metadata |
FALSE (default) returns data. TRUE returns metadata |
Returns respectively: NRF1pair.bam - Bam file contanining reads covering example NRF1 pair binding locus used for SingleMoleculeFootprinting vignette. NRF1pair.bam.bai - Bam index file to Bam file used as example data in SingleMoleculeFootprinting vignette EnrichmentRegions_mm10.rds - GRanges obj of mouse genomic regions enriched for SMF signal in genome-wide capture experiments. Can be used to compute bait capture efficiency ReferenceMethylation.rds - Reference matrix of genome-wide bulk SMF values for published experiments in mouse cell lines AllCs.rds - GRanges obj referencing the genomic context cytosines for mm10
NRF1pair.bam(metadata = TRUE) NRF1pair.bam.bai(metadata = TRUE) EnrichmentRegions_mm10.rds(metadata = TRUE) ReferenceMethylation.rds(metadata = TRUE) AllCs.rds(metadata = TRUE)NRF1pair.bam(metadata = TRUE) NRF1pair.bam.bai(metadata = TRUE) EnrichmentRegions_mm10.rds(metadata = TRUE) ReferenceMethylation.rds(metadata = TRUE) AllCs.rds(metadata = TRUE)