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popularity
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maintenance
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community
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GitHub Stars: 0
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Release Date: Feb 25, 2023
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License

MIT

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Maintenance

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Last Release: 3 years ago
Last Commit: 3 years ago

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Package

Python Versions Compatibility: Unspecified

Age: 3 years
Latest Release: 3 years ago
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Versions: 3
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Readme

Cdiversity: Quantifying B-Cell Clonal Diversity In Repertoire Data

Advances in high-throughput sequencing technologies have enabled the high-throughput characterization of B-cell receptor sequencing data. Still, the accurate identification of clonally related BCR sequences remains a difficult challenge. Importantly, different methods may lead to different clonal definitions, which in turn can affect the quantification of clonal diversity in repertoire data [1]. This library provide different tools and metrics to (i) group B-cell repertoires into clonal groups and (ii) compute diversity indices and diversity profiles from the obtained groups.

Running the analysis

First, you need to install cdiversity, or alternatively you can use the cdiversity.py file provided in the repository:

- pip install cdiversity

Then, you can run a repertoire analysis simulation with the toy example below. For a more complete overview, you can check out Examples/Analyze_sample.py. Briefly, the analysis start by grouping Bcell into clones, and then use the obtained groups to compute various diversity metrics.

(I) Grouping repertoire into clones

Available methods for clonal identification are junction, which simply group clones together only if they have the same junction. Then, there is the commonly used VJ-junction methods, which group together BCR with the same V and J genes, as well as some user-specificed junction similarity (clone_threshold). Finally, the last method is alignfree, which compute tf-idf embedings of the BCRs to perform a fast clustering without relying on the V and J germline genes alignements.

import pandas as pd
import cdiversity

df = pd.read_csv('Data/sample.csv', sep='\t') 
clones_baseline, _ = cdiversity.identify_clonal_group(df, method='junction')
clone_VJJ, _ = cdiversity.identify_clonal_group(df, method='VJJ', clone_threshold = 0.1)

(II) Computing diversity indices

Once the clonal groups are obtained, you can compute any diversity indices or the Hill's diversity profile with a single command. Implemented indices are richness, richness_chao, Shannon_entropy, Shannon_entropy_chao, Simpson_index, dominance, eveness.

from collections import Counter

	clone_dict = Counter(clone_VJJ)
	diversity = cdiversity.Shannon_entropy_Chao(clone_dict)
	div_profile, alpha_axis = cdiversity.diversity_profile(clone_dict)

References

[1] Pelissier, A, Luo, S, et al. "Quantifying B Cell Clonal Diversity In Repertoire Data". Submitted to Frontier in immunology (2022) [Preprint]

FAQs

What is cdiversity?

Quantifying B-Cell Clonal Diversity In Repertoire Data. Visit Snyk Advisor to see a full health score report for cdiversity, including popularity, security, maintenance & community analysis.

Is cdiversity popular?

The python package cdiversity receives a total of 43 weekly downloads. As such, cdiversity popularity was classified as limited. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is cdiversity well maintained?

We found indications that cdiversity is an Inactive project. See the full package health analysis to learn more about the package maintenance status.

Is cdiversity safe to use?

While scanning the latest version of cdiversity, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 19 November-2025, at 05:39 (UTC).

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cdiversity

Quantifying B-Cell Clonal Diversity In Repertoire Data For more information about how to use this package see README

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Readme

Cdiversity: Quantifying B-Cell Clonal Diversity In Repertoire Data

Running the analysis

(I) Grouping repertoire into clones

(II) Computing diversity indices

References

FAQs

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Is cdiversity popular?

Is cdiversity well maintained?

Is cdiversity safe to use?

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Readme

Cdiversity: Quantifying B-Cell Clonal Diversity In Repertoire Data

Running the analysis

(I) Grouping repertoire into clones

(II) Computing diversity indices

References

FAQs

What is cdiversity?

Is cdiversity popular?

Is cdiversity well maintained?

Is cdiversity safe to use?

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