Metadata-Version: 2.4
Name: multiqc_dumpling
Version: 0.4
Summary: MultiQC plugin for Dumpling DMS pipeline
Author-email: Christian Macdonald <christian.macdonald@wisc.edu>
License: MIT
Project-URL: Homepage, https://github.com/odcambc/MultiQC_dumpling
Project-URL: Repository, https://github.com/odcambc/MultiQC_dumpling
Project-URL: Downloads, https://github.com/odcambc/MultiQC_dumpling/releases
Keywords: bioinformatics,multiqc,dumpling,dms
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: JavaScript
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: multiqc>=1.0
Requires-Dist: pandas
Dynamic: license-file

# MultiQC_dumpling Module

## Description
This is a plugin for [MultiQC](https://github.com/ewels/MultiQC) for conducting analysis and quality control of deep mutational scanning libraries with [DIMPLE](https://github.com/coywil26/DIMPLE) and [dumpling](https://github.com/odcambc/dumpling).
This plugin specifically parses baseline library sequencing runs to check for successful library generation.

## Metrics and plots
This plugin generates several QC metrics and plots for baseline library sequencing runs:
### Metrics
- **Mean counts**: The mean and median number of times each variant is observed in a sequencing run.
- **Number of zero counts**: The number of variants that were not observed in a sequencing run.
- **Fraction of zero counts**: The fraction of variants that were not observed in a sequencing run (0-1).
- **Mean and median sequencing depth**: The mean and median number of times each variant at a position was sampled in a sequencing run (i.e., the coverage).
- **Maximum and minimum sequencing depth**: The maximum and minimum number of times each variant at a position was sampled in a sequencing run (i.e., the coverage).
### Plots
- **Variant counts**: A histogram of the number of times each variant is observed in a sequencing run.
- **Coverage**: A histogram of the number of times each variant at a position was sampled in a sequencing run (i.e., the read depth).

Other metrics and plugins that are generated by the dumpling pipeline are also included in the MultiQC report.

## Installation
To install the MultiQC_dumpling module, use pip:
```bash
pip install multiqc_dumpling
```

## Usage
This module is intended for use as part of the [dumpling pipeline](https://github.com/odcambc/dumpling).

To run it manually, some additional files are necessary.

First, provide a `multiqc_config.yaml` file with the following contents:

-**orf**: the nucleotide coordinates of the orf in the reference sequence in the form "start-end". If you are not doing mapping, just provide the length of the orf as "1-length".
-**variants_file**: a csv containing the designed or expected variants in the library. The dumpling/DIMPLE workflows automatically generate this file. If you are providing your own, this should have at least a "pos" column with the amino-acid position of the variant and a "hgvs" column with the variant in HGVS format.

## License
This project is licensed under the MIT License.

## Getting help

For any issues, please open an issue on the GitHub repository. For
questions or feedback, [email Chris](https://www.waymentsteelelab.org).
