Package 'PTMsToPathwaysData'

Title: ExperimentHub Data for PTMsToPathways
Description: Companion data package for PTMsToPathways that registers large post-translational modification data resources and intermediate processed data for vignettes in ExperimentHub.
Authors: Lucia Williams [aut, cre] (ORCID: <https://orcid.org/0000-0003-3785-0247>), Mark Grimes [aut] (ORCID: <https://orcid.org/0000-0003-2673-5892>)
Maintainer: Lucia Williams <[email protected]>
License: GPL (>= 3)
Version: 0.99.4
Built: 2026-10-01 12:12:03 UTC
Source: https://github.com/BiocStaging/PTMsToPathwaysData

Help Index

PTMsToPathwaysData: ExperimentHub Data for PTMsToPathways

Description

Companion ExperimentHub data package for PTMsToPathways. It provides raw, intermediate, and derived data resources used in the PTMsToPathways vignettes and examples.

Details

Available data resources include:

Getting started vignette:

  • AlldataPTMs.txt and ex_full_ptm_table.rda

Raw data processing vignette:

  • phospho_cleaned_mapped.txt and newphos.rda

Cytoscape graphing vignette:

  • FunctionKey.txt and function_key.rda

BRCA Networks vignette:

  • bioplanet_pathway_June2025.csv and bioplanet_pathways.rda

  • PhosphoDiscoData_mmc9.txt

  • brca_clusterlist_data.rda

  • brca_CCCN_data.rda

  • BRCA_stringdb.edges.rda

  • BRCA_genemania.edges.rda

  • BRCA_PCN.data.rda

Use PTMsToPathwaysData() to query the ExperimentHub records registered by this package.

Author(s)

Maintainer: Lucia Williams [email protected] (ORCID)

Authors:

See Also

Useful links:

Examples

eh <- ExperimentHub::ExperimentHub()
query(eh, "PTMsToPathwaysData")

Query PTMsToPathways Data Resources in ExperimentHub

Description

Returns ExperimentHub records tagged for PTMsToPathways BRCA data.

Usage

PTMsToPathwaysData()

Value

A subsetted ExperimentHub object.

Examples

ptm_data <- PTMsToPathwaysData()
ptm_data