II.
LibraryProcess overview
Reference · livelib-process:bioinformatics--spatial-transcriptomics
spatial-transcriptomics overview
Spatial Transcriptomics Analysis - Analysis of spatially-resolved transcriptomics data to understand gene expression patterns in tissue context. Integrates with histological imaging for comprehensive tissue characterization.
Attributes
displayName
spatial-transcriptomics
description
Spatial Transcriptomics Analysis - Analysis of spatially-resolved transcriptomics data
to understand gene expression patterns in tissue context. Integrates with histological imaging
for comprehensive tissue characterization.
libraryPath
library/specializations/domains/science/bioinformatics/spatial-transcriptomics.js
specialization
bioinformatics
references
- - Squidpy: https://squidpy.readthedocs.io/ - SpatialDE: https://github.com/Teichlab/SpatialDE - STUtility: https://ludvigla.github.io/STUtility_web_site/ - Cell2location: https://cell2location.readthedocs.io/
example
const result = await orchestrate('specializations/domains/science/bioinformatics/spatial-transcriptomics', {
projectName: 'Tumor Microenvironment Study',
samples: [{ id: 'sample1', dataPath: '/data/spatial' }],
platform: 'Visium',
histologyImages: ['/images/HE_sample1.tiff']
});
usesAgents
- general-purpose
Outgoing edges
lib_applies_to_domain1
- domain:bioinformatics·DomainBioinformatics
lib_belongs_to_specialization2
- specialization:biomedical-informatics·SpecializationBiomedical Informatics
- specialization:bioinformatics·SpecializationBioinformatics
lib_implements_workflow1
- workflow:experiment-design·WorkflowExperiment Design
lib_involves_role2
- role:research-engineer·RoleResearch Engineer
- role:biomedical-engineer·RoleBiomedical Engineer
lib_requires_skill_area3
- skill-area:data-analysis·SkillAreaData Analysis
- skill-area:statistical-analysis·SkillAreaStatistical Analysis
- skill-area:python-data-pipelines·SkillAreaPython Data Pipelines
Incoming edges
None.