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plate-planner

Python package to create multi-well plate layouts for specimen sample data. Automatically distributes quality control samples according to scheme in config file.

https://github.com/ssi-dk/cd-mrg-plateplanner

Science Score: 44.0%

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
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.0%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Python package to create multi-well plate layouts for specimen sample data. Automatically distributes quality control samples according to scheme in config file.

Basic Info
  • Host: GitHub
  • Owner: ssi-dk
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 45.2 MB
Statistics
  • Stars: 4
  • Watchers: 3
  • Forks: 1
  • Open Issues: 3
  • Releases: 3
Created about 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

PyPI - Version PyPI - Python Version pages-build-deployment .github/workflows/draft-pdf.yml

.github/workflows/publish-to-pypi

PlatePlannerLogo

  • Dynamic QC Sample Patterns: Create plate layouts with customizable QC sample patterns.
  • Flexible Sample Distribution: Distribute samples within groups across plates, accommodating variable numbers of samples per group.
  • Non-Split/Split Group Handling: Control over distributing samples within groups without splitting them over plates or splitting when necessary.
  • Customizable Run Lists & Plate Visualizations: Generate run lists and visualize plate assignments.
  • Block Randomization: Perform sample randomizaition or sample block randomization to prevent run order bias.

Installation

To install PlatePlanner, simply run:

console pip install plate-planner

Documentation

For more detailed documentation, visit PlatePlanner Documentation.

Quick Start Guide

Here's a quick example of how to use PlatePlanner:

```py from plate-planner import Study, QCPlate

Create a study and load your file with sample records (csv, xls/xlsx)

studywithqc = Study(name="cancer") studywithqc.loadspecimenrecords( recordsfile="./data/studysamples.csv", samplegroupidcolumn="pairID", sampleidcolumn="specimen_ID" )

Block randomize groups

studywithqc.randomizeorder(casecontrol=True, reproducible=False)

Distribute samples to a 96-well plate with QC samples as defined in the toml file

qcplate = QCPlate(platedim=(8, 12), QCconfig="./data/plateconfigdynamic.toml") studywithqc.distributesamplestoplates(platelayout=qcplate)

Create visualization for plate 3

fig = studywithqc[2].asfigure( colormetadatakey="organ", annotationmetadatakey="dateof_birth", rotation=45, )

``` Alt text

```py

mshow distribution of sample attribute across all plates

fig = studywithqc.plotattributeplatedistributions(attribute="organ", normalize=True, pltstyle="fivethirtyeight")

```

attribute distribution across plates visualization example

Contributing

We welcome contributions to PlatePlanner! Please read our Contributing Guidelines for more information on how to get involved.

License

PlatePlanner is distributed under the terms of the MIT license.

Owner

  • Name: Statens Serum Institut
  • Login: ssi-dk
  • Kind: organization
  • Location: Denmark

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Ljung"
  given-names: "Filip"
  orcid: "https://orcid.org/0000-0001-7859-8047"
title: "PlatePlanner"
version: 0.2.0
url: "https://github.com/ssi-dk/CD-MRG-PlatePlanner"

GitHub Events

Total
  • Watch event: 1
  • Push event: 1
Last Year
  • Watch event: 1
  • Push event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 190
  • Total Committers: 1
  • Avg Commits per committer: 190.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
filippersson f****n@g****m 190

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 0
  • Total pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.11
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 3
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • dependabot[bot] (6)
  • filippersson (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (6)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 10 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
pypi.org: plate-planner

A tool to create and visualize sample layouts for multiwell plates.

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 10 Last month
Rankings
Dependent packages count: 10.0%
Average: 37.9%
Dependent repos count: 65.9%
Maintainers (1)
mzfilip
Last synced: 8 months ago

Dependencies

pyproject.toml pypi
  • matplotlib *
  • numpy *
  • pandas *
  • tomli *
.github/workflows/publish-to-pypi.yml actions
  • actions/checkout v2 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/build-and-release.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • softprops/action-gh-release v1 composite
.github/workflows/draft-pdf.yml actions
  • actions/checkout v4 composite
  • actions/upload-artifact v1 composite
  • openjournals/openjournals-draft-action master composite
.github/workflows/python-package-conda.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
webapp/requirements.txt pypi