RLHub-package: Accessing RLHub data

In Bishop-Laboratory/RLHub: An ExperimentHub package for accessing processed RLSuite data sets

Description

RLHub provides convenient access point to the processed datasets available within RLBase. In this document, we list the available accessor functions which streamline access to the data.

Details

The RLHub package provides a useful interface to the data stored within the "RLHub" ExperimentHub database. The full manifest of available data is found here:

Title	Accessor	Description
Primary Genomic Annotations (hg38)	annots_primary_hg38	Primary Human genomic annotations curated for use with RLSuite.
Primary Genomic Annotations (mm10)	annots_primary_mm10	Primary Mouse genomic annotations curated for use with RLSuite.
Full Genomic Annotations (hg38)	annots_full_hg38	Full Human genomic annotations curated for use with RLSuite.
Full Genomic Annotations (mm10)	annots_full_mm10	Full Mouse genomic annotations curated for use with RLSuite.
R-loop Binding Proteins	rlbps	R-loop-binding proteins discovered from mass-spec studies.
Gene Expression	gene_exp	Gene expression count tables from matched RNA-Seq experiments corresponding to R-loop profiling. The counts, TPM, and VST-transformed counts are provided.
Feature Enrichment per Sample	feat_enrich_samples	Genomic feature enrichment stats for each peakset in RLBase.
Feature Enrichment per RL-Region	feat_enrich_rlregions	Genomic feature enrichment stats for the RL-Regions in RLBase.
GS-Signal	gs_signal	Bin-level read counts for RLBase samples around R-loop sites discovered using long-read SMRF-Seq (gold-standard sites).
FFT-Model	fft_model	Stacked classifier for deciding whether samples successfully mapped R-loops.
Feature-Prep Model	prep_features	Model for transforming dataset features prior to classification.
RLFS-Test Results	rlfs_res	The results from RLFS (R-loop-forming sequences) analysis on all RLBase samples via the RLSeq package.
RLRegion Annotations	rlregions_annot	R-loop regions (rlregions) derived from S9.6-based and dRNH-based samples ('All' group), annotated with genomic features.
RLRegion Metadata	rlregions_meta	R-loop regions (rlregions) derived from S9.6-based and dRNH-based samples ('All' group), with descriptive metadata.
RLRegion Read Counts	rlregions_counts	Read count tables from RLBase samples quantified across the R-loop regions (rlregions) derived from both S9.6-based and dRNH-based samples ('All' group).
RLBase Sample Manifest	rlbase_samples	The hand-curated manifest of all RLBase samples with descriptive metadata and some sample-level analysis results.

Author(s)

Maintainer: Henry Miller [e-mail] (ORCID) [copyright holder]

Other contributors:

• Alexander Bishop [e-mail] (ORCID) [thesis advisor, copyright holder]

See Also

Useful links:

• https://github.com/Bishop-Laboratory/RLHub

• https://bishop-laboratory.github.io/RLHub/

• Report bugs at https://github.com/Bishop-Laboratory/RLHub/issues

Bishop-Laboratory/RLHub documentation built on Jan. 20, 2022, 3:47 p.m.