@platforma-open/milaboratories.repertoire-diversity-2 3.0.0 → 3.1.0

package/block-pack/CHANGELOG.md

@@ -0,0 +1,331 @@
+# @platforma-open/milaboratories.repertoire-diversity-2
+
+## 3.1.0
+
+### Minor Changes
+
+- f0f5261: Migrate onto the block-tools structurer (full SDK upgrade: model/ui-vue 1.79.14,
+  workflow-tengo 6.6.3, tengo-builder 4.0.8) and BlockModelV3.
+
+  Persisted state is preserved via the legacy upgrader. UI bindings move to
+  `app.model.data`; the metric list (`MetricUI[]`) now lives in `data` and is
+  projected to the workflow's `Metric[]` by the args lambda — the debounced
+  ui→args sync watcher is gone. Block labels and table/graph view state are
+  UI-only and no longer stale the block; only the abundance input and metric set
+  do.
+
+## 3.0.1
+
+### Patch Changes
+
+- 453cb59: Rename block
+
+## 3.0.0
+
+### Major Changes
+
+- a96467f: Support peptides
+- be69712: Support peptides
+
+### Patch Changes
+
+- Updated dependencies [a96467f]
+- Updated dependencies [be69712]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@2.0.0
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@2.0.0
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@2.0.0
+
+## 2.0.36
+
+### Patch Changes
+
+- 7c6a978: update dependencies
+- Updated dependencies [7c6a978]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.5.9
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.6.9
+
+## 2.0.35
+
+### Patch Changes
+
+- 80689b6: SDK Update
+
+## 2.0.34
+
+### Patch Changes
+
+- Updated dependencies [216f552]
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.6.8
+
+## 2.0.33
+
+### Patch Changes
+
+- Updated dependencies [bc865e3]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.5.8
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.6.7
+
+## 2.0.32
+
+### Patch Changes
+
+- Updated dependencies [8f000f8]
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.6.6
+
+## 2.0.31
+
+### Patch Changes
+
+- Updated dependencies [08ea006]
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.6.5
+
+## 2.0.30
+
+### Patch Changes
+
+- Updated dependencies [20e60a4]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.5.7
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.6.4
+
+## 2.0.29
+
+### Patch Changes
+
+- Updated dependencies [c85fbd0]
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.6.4
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.5.6
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.6.3
+
+## 2.0.28
+
+### Patch Changes
+
+- d157baf: Show running state for tables and graphs, migrate to new project template
+- Updated dependencies [d157baf]
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.6.3
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.5.5
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.6.2
+
+## 2.0.27
+
+### Patch Changes
+
+- 63c4b69: technical release
+- Updated dependencies [63c4b69]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.5.4
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.6.1
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.6.2
+
+## 2.0.26
+
+### Patch Changes
+
+- e13e703: Block metadata updated.
+
+## 2.0.25
+
+### Patch Changes
+
+- Updated dependencies [8d7b553]
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.6.0
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.6.1
+
+## 2.0.24
+
+### Patch Changes
+
+- 48ff0ed: Update SDK
+
+## 2.0.23
+
+### Patch Changes
+
+- Updated dependencies [f3b07e5]
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.5.5
+
+## 2.0.22
+
+### Patch Changes
+
+- Updated dependencies [192909e]
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.6.0
+
+## 2.0.21
+
+### Patch Changes
+
+- 3e39f73: technical release
+- 37c4e58: technical release
+- 7c4d608: technical release
+- a2200a0: technical release
+- Updated dependencies [3e39f73]
+- Updated dependencies [37c4e58]
+- Updated dependencies [7c4d608]
+- Updated dependencies [a2200a0]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.5.3
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.5.4
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.5.4
+
+## 2.0.20
+
+### Patch Changes
+
+- Updated dependencies [d0287b6]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.5.2
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.5.3
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.5.3
+
+## 2.0.19
+
+### Patch Changes
+
+- 6ff86d7: Updated SDK
+- Updated dependencies [6ff86d7]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.5.1
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.5.2
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.5.2
+
+## 2.0.18
+
+### Patch Changes
+
+- @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.5.1
+
+## 2.0.17
+
+### Patch Changes
+
+- Updated dependencies [5cf567c]
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.5.1
+
+## 2.0.16
+
+### Patch Changes
+
+- Updated dependencies [365f92f]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.5.0
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.5.0
+
+## 2.0.15
+
+### Patch Changes
+
+- Updated dependencies [057ca18]
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.5.0
+
+## 2.0.14
+
+### Patch Changes
+
+- Updated dependencies [13f110e]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.4.0
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.4.0
+
+## 2.0.13
+
+### Patch Changes
+
+- f95c059: Update SDK
+- Updated dependencies [f95c059]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.3.1
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.3.1
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.4.1
+
+## 2.0.12
+
+### Patch Changes
+
+- Updated dependencies [60f2dc1]
+- Updated dependencies [1b4bc1d]
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.4.0
+
+## 2.0.11
+
+### Patch Changes
+
+- @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.3.1
+
+## 2.0.10
+
+### Patch Changes
+
+- Updated dependencies [c16a9dc]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.3.0
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.3.0
+
+## 2.0.9
+
+### Patch Changes
+
+- Updated dependencies [7bc102b]
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.3.0
+
+## 2.0.8
+
+### Patch Changes
+
+- Updated dependencies [0888e31]
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.2.0
+
+## 2.0.7
+
+### Patch Changes
+
+- Updated dependencies [6dff400]
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.2.1
+
+## 2.0.6
+
+### Patch Changes
+
+- Updated dependencies [84296a7]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.2.0
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.2.0
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.1.3
+
+## 2.0.5
+
+### Patch Changes
+
+- 965efa9: Updated block metadata
+
+## 2.0.4
+
+### Patch Changes
+
+- afe71a0: Update SDK
+
+## 2.0.3
+
+### Patch Changes
+
+- 6dba4b4: Fix package name
+- Updated dependencies [6dba4b4]
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.1.2
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.1.2
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.1.2
+
+## 2.0.2
+
+### Patch Changes
+
+- 1417619: Init
+- Updated dependencies [1417619]
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.1.1
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.1.1
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.1.1
+
+## 2.0.1
+
+### Patch Changes
+
+- Updated dependencies [1d45e7d]
+  - @platforma-open/milaboratories.repertoire-diversity-2.workflow@1.1.0
+  - @platforma-open/milaboratories.repertoire-diversity-2.model@1.1.0
+  - @platforma-open/milaboratories.repertoire-diversity-2.ui@1.1.0
+
+## 2.0.0
+
+### Major Changes
+
+- f6e02ad: init

package/block-pack/description.md

@@ -0,0 +1,5 @@
+# Overview
+
+Calculates comprehensive diversity metrics for any VDJ clonotype repertoires (TCR, BCR) or peptide phage display libraries to characterize and compare diversity across samples. The block reads abundance counts from upstream blocks (MiXCR, peptide-extraction, ...) and computes multiple standard diversity indices: observed richness (number of unique sequences), richness estimators (Chao1, Efron-Thisted), evenness indices (Shannon-Wiener, Inverse Simpson), and dominance measures (D50, Gini).
+
+To ensure fair comparisons between samples with different sequencing depths, the block supports normalization methods including selecting the most abundant sequences or statistically downsampling to a common size using hypergeometric sampling before calculating diversity metrics. This enables robust comparison of sequence diversity across experimental conditions, time points, or treatment groups, helping identify changes in immune repertoire or peptide library composition associated with disease, vaccination, or therapeutic interventions.

package/block-pack/manifest.json

@@ -0,0 +1 @@
+{"schema":"v2","description":{"id":{"organization":"milaboratories","name":"repertoire-diversity-2","version":"3.1.0"},"components":{"workflow":{"type":"workflow-v1","main":{"type":"relative","path":"main.plj.gz"}},"model":{"type":"relative","path":"model.json"},"ui":{"type":"relative","path":"ui.tgz"}},"meta":{"title":"Diversity Analysis","description":"Calculates diversity metrics — richness estimators (Chao1, Efron-Thisted), evenness indices (Shannon-Wiener, Inverse Simpson), and dominance measures (D50, Gini) — to characterize clonotype or peptide library composition across samples.","longDescription":{"type":"relative","path":"description.md"},"changelog":{"type":"relative","path":"CHANGELOG.md"},"logo":{"type":"relative","path":"block-logo.png"},"url":"https://github.com/platforma-open/repertoire-diversity","docs":"https://docs.platforma.bio/guides/vdj-analysis/diversity-analysis/","support":"mailto:support@milaboratories.com","tags":["airr","downstream","repertoire","peptide"],"organization":{"name":"MiLaboratories Inc","url":"https://milaboratories.com/","logo":{"type":"relative","path":"organization-logo.png"}},"marketplaceRanking":16600},"featureFlags":{"supportsLazyState":true,"supportsPframeQueryRanking":true,"requiresUIAPIVersion":3,"requiresModelAPIVersion":2,"requiresCreatePTable":2,"requiresPFramesVersion":1001031,"requiresPFrameSpec":true,"requiresPFrame":true,"requiresDialog":true,"requiresColumnsCollection":true}},"timestamp":1784562706330,"files":[{"name":"main.plj.gz","size":478762,"sha256":"F0D2F321FEC5CA2ACF6310A6A1D372DBCC65428BF0F7AE46AC788230593ABFDC"},{"name":"model.json","size":493325,"sha256":"D5BD8FF739F06E25F1B23C19C8D022F30AACA77F26CFC306A17FBB50665C6793"},{"name":"ui.tgz","size":6357438,"sha256":"0F0A4F89BE1496C7FD32244D0A10687C25D1250DB2C55FA06BC211C8E33AB7FF"},{"name":"organization-logo.png","size":24439,"sha256":"FA71390C77C91E4B7FAAE5640D00F92F1E3F2869296F68B6040DD7CC549A50B5"},{"name":"description.md","size":1052,"sha256":"23D0A0CA09852966C956D93AA6FE471C1EA4DCBF60405160D6EE381412AE771D"},{"name":"CHANGELOG.md","size":7983,"sha256":"463EFC5FCF8329B02AFF024C896EA0C942FCC8D97E05B0B3B4C963AA756A0E7C"},{"name":"block-logo.png","size":21527,"sha256":"6BB33BAF0CD039549661B51AE490373BE60D1811EC71F5023400928293BC2427"}]}