HuBMAPR: an R client for the HuBMAP data portal.
Christine Hou1, Shila Ghazanfar2,3,4, Federico Marini5,6
1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, United States.
Bioinformatics Advances
|April 11, 2025
Summary
Researchers can now access human body cellular data more easily using HuBMAPR, an R client for the Human BioMolecular Atlas Program (HuBMAP) Data Portal. This tool streamlines data discovery and retrieval for biological research.
Area of Science:
- Biomedical research
- Genomics
- Cellular biology
Background:
- The Human BioMolecular Atlas Program (HuBMAP) aims to create a comprehensive, accessible platform for studying the human body at the cellular level.
- The HuBMAP Data Portal offers diverse datasets generated using advanced experimental technologies with spatial resolution.
Purpose of the Study:
- To enhance accessibility of the HuBMAP Data Portal for researchers.
- To introduce HuBMAPR, an R client designed for programmatic interaction with HuBMAP data.
Main Methods:
- Development of an R client package named HuBMAPR.
- Integration of HuBMAPR with the Bioconductor repository for easy installation and use.
Main Results:
- HuBMAPR provides an efficient interface for discovering and retrieving HuBMAP data.
- The R client simplifies programmatic access to complex, high-resolution spatial biological data.
Conclusions:
- HuBMAPR significantly improves the usability and accessibility of the HuBMAP Data Portal for the research community.
- The R package facilitates faster and more efficient analysis of human cellular data, advancing biomedical research.
More Related Videos
Related Concept Videos
01:42Microtubule Associated Proteins (MAPs)
4.8K
Microtubule function and architecture are regulated by an array of specialized proteins called microtubule-associated proteins or MAPs. These proteins are widespread across different organisms and have conserved protein motifs, like the multi-TOG domain for tubulin binding found in the CLASP family of MAPs. Some MAPs are lineage-specific based on their conserved domains. Their functions depend upon the cytoskeletal architecture and cell type they are located within. In-plant cells, a specific...
4.8K
01:02The R Chart
508
In statistical process control, control charts, particularly R charts, are instrumental in monitoring process variations and identifying non-random patterns that run charts might miss. R charts track the variability within process subgroups, which is crucial when standard deviation use is impractical or unknown process variations exist.
R charts are pivotal for pinpointing shifts in process variability. Stability is indicated when all data points remain within the defined upper and lower...
R charts are pivotal for pinpointing shifts in process variability. Stability is indicated when all data points remain within the defined upper and lower...
508
01:22Interpreting R Charts
504
R chart, or range chart, is a fundamental tool in statistical process control used to monitor the variability within a process. It complements the X-bar (x̄) chart by focusing on the range of the data, rather than individual values, providing a clear picture of the process dispersion over time.
An R chart plots the range of subsets of measurements collected from a process. Each point on the chart represents the range—defined as the difference between the maximum and minimum...
An R chart plots the range of subsets of measurements collected from a process. Each point on the chart represents the range—defined as the difference between the maximum and minimum...
504
01:28Introduction to GIS
804
Geographic Information Systems (GIS) are tools for storing, analyzing, and displaying spatial data alongside related attributes. Unlike traditional information systems that address general queries, GIS incorporates spatial components, enabling users to answer "where" and "how far." For example, GIS can process housing data linked to geographic locations like zip codes, allowing insights into population density or housing distribution through thematic maps.GIS integrates technologies such as...
804
01:29Levels of Use of a GIS
511
Geographic Information Systems (GIS) operate across three levels of application, each representing an increasing degree of complexity: data management, analysis, and prediction. These levels reflect the expanding functionality and versatility of GIS technology in handling spatial data for diverse purposes.Data ManagementAt its foundational level, GIS serves as a tool for data management, enabling the input, storage, retrieval, and organization of spatial data. This level is often employed in...
511
01:23GIS Software, Hardware, and Sources of GIS Data
1.0K
A Geographic Information System (GIS) combines specialized software and hardware to effectively manage, analyze, and present spatial and related data. GIS software includes critical functionalities such as a user interface for easy navigation, database management tools for handling spatial and attribute data, and data retrieval features for efficient access. Analytical tools transform raw data into insights, while display functions produce maps and reports in various formats for effective...
1.0K