bcell_memory_formation

https://github.com/michael-swift/bcell_memory_formation

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
Links to: biorxiv.org
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Academic email domains
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: michael-swift
Language: Jupyter Notebook
Default Branch: main
Size: 391 MB

Statistics

Stars: 0
Watchers: 1
Forks: 1
Open Issues: 0
Releases: 0

Created about 4 years ago · Last pushed over 1 year ago

Metadata Files

Readme Citation

Long-term B cell memory emerges at uniform relative rates in the human immune response

Code repository accompanying the paper "Long-term B cell memory emerges at uniform relative rates in the human immune response" by Cvijović, Swift, and Quake.

Overview

This repository contains the analysis code and workflows used in our study of B cell memory formation dynamics across human immune tissues.

Data Availability

Raw sequencing data is available at NCBI under accession number PRJNA1203354.

Repository Structure

snakemake_workflow/: Contains the Snakemake pipeline for data pre-processing and analysis
CITATION.cff: Citation information for this repository
README.md: This file
analysis: Contains the secondary analyses done on pre-processed data that could be used to reproduce the figures in the paper

Publication

Preprint available on bioRxiv: https://www.biorxiv.org/content/10.1101/2023.11.27.568934v2

Disclaimer

This software is provided as-is for research reproducibility purposes. While we aim to be helpful, we make no guarantees about providing ongoing support or maintenance for the code in this repository.

License

MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Owner

Name: mswift
Login: michael-swift
Kind: user
Location: Palo Alto

Repositories: 2
Profile: https://github.com/michael-swift

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this repository, please cite it as below."
authors:
  - family-names: Cvijović
    given-names: Ivana
    affiliation: "Department of Applied Physics, Stanford University"
  - family-names: Swift
    given-names: Michael
    affiliation: "Department of Chemical and Systems Biology, Stanford University"
  - family-names: Quake
    given-names: Stephen R.
    affiliation: "Department of Applied Physics, Stanford University"
title: "Long-term B cell memory emerges at uniform relative rates in the human immune response"
version: 1.0.0
date-released: 2024-01-23
url: "https://github.com/michael-swift/Bcell_memory_formation"
repository-code: "https://github.com/michael-swift/Bcell_memory_formation"
preferred-citation:
  type: article
  authors:
    - family-names: Cvijović
      given-names: Ivana
    - family-names: Swift
      given-names: Michael
    - family-names: Quake
      given-names: Stephen R.
  title: "Long-term B cell memory emerges at uniform relative rates in the human immune response"
  year: 2024
  journal: "bioRxiv"
  doi: "10.1101/2023.11.27.568934"
  url: "https://www.biorxiv.org/content/10.1101/2023.11.27.568934v2"

GitHub Events

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Push event: 1
Public event: 1
Fork event: 1

Last Year

Push event: 1
Public event: 1
Fork event: 1

Dependencies

snakemake_workflow/scripts/vdj/cython_packages/setup.py pypi

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science