Science Score: 44.0%
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✓codemeta.json file
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○Scientific vocabulary similarity
Low similarity (7.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: pesho-ivanov
- License: mpl-2.0
- Language: Jupyter Notebook
- Default Branch: main
- Size: 27.6 MB
Statistics
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Gene-level analysis of lymphocyte single-cell RNA data based on a clonality specification language
CellDive (src/) is a tool for exploring clonality of lymphocytes and differential expression based on single-cell RNA-seq:
* clonality rules specification based on the alpha and beta chains of T-cell and B-cell receptors (TCR and BCR)
* clustering into main-clone, related-to-main-clone, bystander groups and single bystanders based on the clonal rules
* bipartite graph visualization of the full clonality information from the samples
* differential expression (DE) between specified clones within the same sample (no batch effects!)
* gene sets overview accross samples and DE methods
CellDive has been applied (example/) to a dozen of human cutaneous lymphoma samples. The clonality rules were used to partition each sample into a malignant clone (main-clone) and healthy cells (bystanders). Differential expression analyses was applied to the two clusters (no batch effect).
Workflow
Contributions
Pesho Ivanov (advisor Martin Vechev), Software Reliability Lab, ETH Zurich: * code and execution * alpha and beta chain language rules for specifying clones. each cell is colored depending on the clone * bipartite graph with left nodes for alpha-chains, right nodes for beta-chains, and cells as edges (possibly connected to No-alpha and No-beta nodes)
Data used to produce example/, Department of Dermatology, University Hospital Zurich: * Yun-Tsan, Desislava Ignatova, Emmanuella Guenova
Note: The code has been written in 2017--2018 so it may be outdated.
Owner
- Name: Pesho Ivanov
- Login: pesho-ivanov
- Kind: user
- Location: State College
- Company: Penn State
- Website: pesho-ivanov.github.io
- Twitter: peshotrie
- Repositories: 31
- Profile: https://github.com/pesho-ivanov
Comp.Bio postdoc @ Penn State; PhD from ETH Zurich: Optimal sequence alignment using A*
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: 'CellDive: Gene-level analysis of lymphocyte single-cell RNA data based on a clonality specification language'
message: 'If you use this software, please cite it as below.'
type: software
authors:
- family-names: Ivanov
given-names: Pesho
orcid: 'https://orcid.org/0000-0002-8119-3849'
email: ivanov@pesho.info
- family-names: Vechev
given-names: Martin
orcid: 'https://orcid.org/0000-0002-0054-9568'
url: 'https://github.com/pesho-ivanov/celldive'
abstract: >-
CellDive: Gene-level analysis of lymphocyte single-cell
RNA data based on a clonality specification language
keywords:
- single cell
- RNA sequencing
- TCR
- BCR
- clonality
- differential expression
- alpha and beta chains
license: MPL-2.0
version: 1.0.0
date-released: '2023-03-03'
GitHub Events
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