Introduction | Installation | Build and inspect a segmentation set | Correspondence across segmentations | Categorical cell-state stability | Reading support sensitivity | Optional spatial evidence | Agreement among segmentation runs | Interoperability and interpretation | A qualified Xenium application
Package: SegStability 0.99.0
Rama Krishna Pudota
SegStability: Descriptive Segmentation Sensitivity in Spatial Transcriptomics
Quantifies correspondence between alternative cell segmentations of the same molecule-resolved spatial transcriptomics experiment. Preserves an immutable molecule universe, exact molecule identities, complete cell censuses, and explicit assignment statuses when constructing weighted shared-molecule graphs. Describes categorical cell-state stability, directional support sensitivity, optional spatial topology and polygon overlap, and agreement among stochastic segmentation runs. Results describe sensitivity to segmentation choices and do not estimate segmentation accuracy or establish biological ground truth.
Authors:
SegStability_0.99.0.tar.gz
SegStability_0.99.0.zip(r-4.7-any)SegStability_0.99.0.zip(r-4.6-any)SegStability_0.99.0.zip(r-4.5-any)
SegStability_0.99.0.tgz(r-4.6-any)SegStability_0.99.0.tgz(r-4.5-any)
SegStability_0.99.0.tar.gz(r-4.7-any)SegStability_0.99.0.tar.gz(r-4.6-any)
SegStability_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SegStability/json (API)
| # Install 'SegStability' in R: |
| install.packages('SegStability', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ramakrishna-p21/segstability/issues
Datasets:
- segmentationExample - Small synthetic molecule assignments for two segmentations
spatialtranscriptomicssinglecelldatarepresentation
Last updated from:0f5a1bad6d. Checks:1 NOTE, 7 OK, 2 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 182 | ||
| linux-devel | OK | 777 | ||
| source / vignettes | OK | 446 | ||
| linux-release | OK | 519 | ||
| macos-release | OK | 467 | ||
| macos-oldrel | ERROR | 681 | ||
| windows-devel | OK | 694 | ||
| windows-release | OK | 574 | ||
| windows-oldrel | ERROR | 869 | ||
| wasm-release | OK | 146 |
Exports:ambiguityDataanchorTopologyassignmentDataassignmentStatusassignmentSummarycellCensuscellSummarycompareGeometrycompareSegmentationscomponentSummarycorrespondenceEdgesfeatureDatafromMoleculeExperimentgeometryFromSpatialFeatureExperimentmoleculeDataprovenancereplicateAgreementrunMetadatasegmentationInfosegmentationNamesSegmentationPartitionSegmentationSetshowstateStabilitysummarysupportSensitivityvalidateCoordinatesvalidateGeometryvalidateProvenancevalidateSegmentationvalidateSegmentationSet
Dependencies:BiocGenericsdigestgenericsS4Vectors
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Descriptive segmentation sensitivity in spatial transcriptomics | SegStability-package SegStability |
| Describe secondary reciprocal-anchor topology | anchorTopology |
| Describe polygon agreement and derived maximum-IoU matching | compareGeometry |
| Compare two segmentations of one immutable molecule universe | compareSegmentations |
| Import retained molecules with explicit segmentation evidence | fromMoleculeExperiment |
| Extract an explicitly keyed SpatialFeatureExperiment geometry sidecar | geometryFromSpatialFeatureExperiment |
| Public summary of the qualified ovrlpy/Xenium application | ovrlpy_validation_summary |
| Label-invariant agreement among segmentation runs | replicateAgreement |
| Complete descriptive correspondence between two segmentations | assignmentSummary assignmentSummary,SegmentationComparison-method cellSummary cellSummary,SegmentationComparison-method componentSummary componentSummary,SegmentationComparison-method correspondenceEdges correspondenceEdges,SegmentationComparison-method provenance,SegmentationComparison-method SegmentationComparison-class segmentationNames,SegmentationComparison-method show,SegmentationComparison-method summary,SegmentationComparison-method |
| Small synthetic molecule assignments for two segmentations | segmentationExample |
| One segmentation bound to an immutable molecule universe | ambiguityData ambiguityData,SegmentationPartition-method assignmentStatus assignmentStatus,SegmentationPartition-method cellCensus cellCensus,SegmentationPartition-method provenance provenance,SegmentationPartition-method runMetadata runMetadata,SegmentationPartition-method SegmentationPartition SegmentationPartition-class show,SegmentationPartition-method |
| A named collection sharing one immutable molecule universe | assignmentData assignmentData,SegmentationSet-method featureData featureData,SegmentationSet-method moleculeData moleculeData,SegmentationSet-method provenance,SegmentationSet-method segmentationInfo segmentationInfo,SegmentationSet-method segmentationNames segmentationNames,SegmentationSet-method SegmentationSet SegmentationSet-class show,SegmentationSet-method summary,SegmentationSet-method [[,SegmentationSet-method |
| Describe categorical state stability across complete correspondence | stateStability |
| Describe directional support sensitivity of complete correspondence | supportSensitivity |
| Validate molecule coordinates without transformation | validateCoordinates |
| Validate optional cell geometry without repair | validateGeometry |
| Validate provenance shape and completeness | validateProvenance |
| Validate a segmentation partition explicitly | validateSegmentation |
| Validate a shared-universe segmentation set explicitly | validateSegmentationSet |