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Pycashier

Pycashier: cash in on DNA barcode tags - Published in JOSS (2024)

https://github.com/brocklab/pycashier

Science Score: 100.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

bioinformatics pipeline
Last synced: 6 months ago · JSON representation ·

Repository

cash in on DNA barcode tags

Basic Info
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 3
  • Open Issues: 5
  • Releases: 0
Topics
bioinformatics pipeline
Created almost 6 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

Forks Stargazers Issues MIT License PYPI PyVersion Conda ghcr.io joss

Pycashier

Tool for extracting and processing DNA barcode tags from Illumina sequencing.

Default parameters are designed for use by the Brock Lab to process data generated from ClonMapper lineage tracing experiments, but is extensible to other similarly designed tools.

Documentation

See the paper for a high-level overview and the documentation for more in-depth installation and usage instructions.

Getting Started

Installation

Conda

You may use conda, mamba, or micromamba to install pycashier and it's runtime dependencies.

bash micromamba install bioconda::cutadapt bioconda::fastp bioconda::pysam bioconda::starcode conda-forge::pycashier

You can also use the included env.yml to create your environment and install everything you need.

bash wget https://raw.githubusercontent.com/brocklab/pycashier/main/conda/env.yml micromamba create -f env.yml micromamba activate cashierenv

Additionally, you may use pixi to install and use pycashier.

sh pixi init --channel conda-forge --channel bioconda myproject cd myproject pixi add pycashier starcode pysam cutadapt fastp pixi shell

Docker

If you prefer to use use docker you can use the below command.

bash docker run --rm -it -v $PWD:/data -u $(id -u):$(id -g) ghcr.io/brocklab/pycashier

[!NOTE] You should specify a version tag with the image for better reproducibility for example, ghrc.io/brocklab/pycashier:v2024.1001.

Usage

To extract barcodes from targeted sequencing data:

sh pycashier extract -i fastqs -o outs

To combine data from multiple samples and compute basic overlap metrics:

sh pycashier receipt -i outs -o combined.tsv

See pycashier --help and pycashier SUBCMD --help for additional subcommands and options.

Pycashier is open source and licensed under the MIT License.

Owner

  • Name: brocklab
  • Login: brocklab
  • Kind: organization
  • Location: Austin, TX

JOSS Publication

Pycashier: cash in on DNA barcode tags
Published
October 31, 2024
DOI
Volume 9, Issue 102, Page 6891
Authors
Daylin Morgan ORCID
The University of Texas at Austin, United States of America
Amy Brock ORCID
The University of Texas at Austin, United States of America
Editor
Lorena Pantano ORCID
Tags
python sequencing DNA barcoding pipeline
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

cff-version: "1.2.0"
authors:
- family-names: Morgan
  given-names: Daylin
  orcid: "https://orcid.org/0000-0002-4218-2805"
- family-names: Brock
  given-names: Amy
  orcid: "https://orcid.org/0000-0001-8255-9024"
contact:
- family-names: Brock
  given-names: Amy
  orcid: "https://orcid.org/0000-0001-8255-9024"
doi: 10.5281/zenodo.13863889
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Morgan
    given-names: Daylin
    orcid: "https://orcid.org/0000-0002-4218-2805"
  - family-names: Brock
    given-names: Amy
    orcid: "https://orcid.org/0000-0001-8255-9024"
  date-published: 2024-10-31
  doi: 10.21105/joss.06891
  issn: 2475-9066
  issue: 102
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6891
  title: "Pycashier: cash in on DNA barcode tags"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06891"
  volume: 9
title: "Pycashier: cash in on DNA barcode tags"

GitHub Events

Total
  • Issues event: 2
  • Delete event: 1
  • Push event: 7
  • Create event: 1
Last Year
  • Issues event: 2
  • Delete event: 1
  • Push event: 7
  • Create event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 297
  • Total Committers: 3
  • Avg Commits per committer: 99.0
  • Development Distribution Score (DDS): 0.02
Past Year
  • Commits: 37
  • Committers: 1
  • Avg Commits per committer: 37.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Daylin Morgan d****n@g****m 291
DaylinMorgan 4****n 4
Daylin Morgan d****n@g****u 2
Committer Domains (Top 20 + Academic)
gsafcomp01.ccbb.utexas.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 26
  • Total pull requests: 16
  • Average time to close issues: 2 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 0.38
  • Average comments per pull request: 0.0
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 9
  • Pull requests: 7
  • Average time to close issues: 11 days
  • Average time to close pull requests: about 3 hours
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • daylinmorgan (25)
  • aedin (1)
  • AndreaLGardner (1)
Pull Request Authors
  • daylinmorgan (24)
  • aedin (1)
Top Labels
Issue Labels
enhancement (1) documentation (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 53 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 38
  • Total maintainers: 1
pypi.org: pycashier

cash in on expressed barcode tags

  • Versions: 25
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 53 Last month
Rankings
Dependent packages count: 10.0%
Average: 16.7%
Downloads: 18.5%
Dependent repos count: 21.7%
Maintainers (1)
daylinmorgan
Last synced: 6 months ago
conda-forge.org: pycashier
  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Average: 49.1%
Dependent packages count: 51.2%
Forks count: 54.2%
Stargazers count: 57.0%
Last synced: 6 months ago

Dependencies

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.github/workflows/tests.yml actions
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docker/Dockerfile docker
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.github/workflows/release.yml actions
pyproject.toml pypi
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