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aiturbidemil merged 3 commits into from
Nov 15, 2025
Merged

20251115 update block metadata #13

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a6f5fc4
sdk update
aiturbidemil Nov 15, 2025
9b2aa8d
updated metadata
aiturbidemil Nov 15, 2025
c3d0cdb
changeset
aiturbidemil Nov 15, 2025
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5 changes: 5 additions & 0 deletions .changeset/poor-ways-join.md
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---
'@platforma-open/milaboratories.rarefaction': patch
---

Block metadata updated.
3 changes: 2 additions & 1 deletion block/package.json
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"title": "Rarefaction analysis",
"logo": "file:../logos/block-logo.png",
"url": "https://github.com/platforma-open/rarefaction",
"docs": "https://docs.platforma.bio/guides/vdj-analysis/rarefaction/",
"support": "mailto:support@milaboratories.com",
"description": "Performs rarefaction analysis on clonotype data to assess species richness.",
"description": "Performs rarefaction analysis on clonotype data to assess repertoire diversity and compare clonotype richness across samples with different sequencing depths.",
"longDescription": "file:../docs/description.md",
"changelog": "file:../CHANGELOG.md",
"tags": [
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6 changes: 2 additions & 4 deletions docs/description.md
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# Overview

Rarefaction is a technique used to assess species richness from the results of sampling. Specifically, it is used to compare the clonal diversity of immune repertoires of different sizes.
Performs rarefaction analysis on clonotype data from immune receptor repertoires (TCR or BCR) to assess repertoire diversity and compare clonotype richness across samples with different sequencing depths. Rarefaction is a statistical technique that estimates the expected number of unique clonotypes as a function of sampling depth, enabling fair comparison of diversity between repertoires of different sizes.
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medium

The first sentence is quite long and dense. For better readability, consider breaking it into two separate sentences. This will help users quickly grasp the block's primary function and its application.

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Performs rarefaction analysis on clonotype data from immune receptor repertoires (TCR or BCR) to assess repertoire diversity and compare clonotype richness across samples with different sequencing depths. Rarefaction is a statistical technique that estimates the expected number of unique clonotypes as a function of sampling depth, enabling fair comparison of diversity between repertoires of different sizes.
This block performs rarefaction analysis on clonotype data from immune receptor repertoires (TCR or BCR). The analysis is used to assess repertoire diversity and compare clonotype richness across samples with different sequencing depths. Rarefaction is a statistical technique that estimates the expected number of unique clonotypes as a function of sampling depth, enabling fair comparison of diversity between repertoires of different sizes.


This block performs rarefaction analysis on clonotype data. It calculates the mean number of unique clonotypes for various subsampling depths for each sample, providing insight into the clonal richness of the repertoires.

The analysis is based on a random subsampling of clonotypes from each repertoire at different depths. At each depth, the number of unique clonotypes is recorded. This process is repeated multiple times to generate a smooth rarefaction curve, which represents the expected number of unique clonotypes as a function of the number of sampled clonotypes. The shape of the curve can be used to compare the diversity of different repertoires. For example, a steeper curve indicates a higher diversity.
The block processes clonotype count data from VDJ processing blocks and performs random subsampling at multiple depths for each sample. At each subsampling depth, the number of unique clonotypes is recorded, and this process is repeated multiple times to generate smooth rarefaction curves representing the mean expected number of unique clonotypes. The shape and slope of these curves provide insights into repertoire diversity: steeper curves indicate higher diversity and suggest that additional sequencing would reveal more unique clonotypes, while plateauing curves indicate that most diversity has been captured at the current sequencing depth.
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medium

This paragraph describes a sequence of steps. Using a list format would make the process clearer and easier for users to understand at a glance.

Suggested change
The block processes clonotype count data from VDJ processing blocks and performs random subsampling at multiple depths for each sample. At each subsampling depth, the number of unique clonotypes is recorded, and this process is repeated multiple times to generate smooth rarefaction curves representing the mean expected number of unique clonotypes. The shape and slope of these curves provide insights into repertoire diversity: steeper curves indicate higher diversity and suggest that additional sequencing would reveal more unique clonotypes, while plateauing curves indicate that most diversity has been captured at the current sequencing depth.
The block processes clonotype count data from VDJ processing blocks and performs the following steps for each sample:
* Performs random subsampling at multiple depths.
* Records the number of unique clonotypes at each depth.
* Repeats this process multiple times to generate smooth rarefaction curves, which represent the mean expected number of unique clonotypes.
The shape and slope of these curves provide insights into repertoire diversity: steeper curves indicate higher diversity and suggest that additional sequencing would reveal more unique clonotypes, while plateauing curves indicate that most diversity has been captured at the current sequencing depth.

70 changes: 66 additions & 4 deletions pnpm-lock.yaml
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2 changes: 1 addition & 1 deletion pnpm-workspace.yaml
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"@platforma-sdk/model": ^1.45.0
"@platforma-sdk/ui-vue": ^1.45.13
"@platforma-sdk/workflow-tengo": ^5.5.12
"@platforma-sdk/block-tools": ^2.6.16
"@platforma-sdk/block-tools": ^2.6.21
"@platforma-sdk/test": ^1.45.15
"@platforma-sdk/tengo-builder": ^2.3.3
"@platforma-sdk/package-builder": ^3.10.7
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