https://github.com/dirmeier/rnaiutilities

A collection of python modules and command line tools for processing image-based RNAi screens.
https://github.com/dirmeier/rnaiutilities

cellprofiler database microscopy python rnai sqlite

Last synced: about 1 month ago
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A collection of python modules and command line tools for processing image-based RNAi screens.

• Host: GitHub
• URL: https://github.com/dirmeier/rnaiutilities
• Owner: dirmeier
• License: gpl-3.0
• Created: 2019-04-02T19:38:26.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2019-04-02T21:35:09.000Z (about 7 years ago)
• Last Synced: 2025-01-17T06:45:46.846Z (over 1 year ago)
• Topics: cellprofiler, database, microscopy, python, rnai, sqlite
• Language: Python
• Homepage:
• Size: 56 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Code of conduct: code-of-conduct.md

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README

          
# rnaiutilities 

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A collection of python modules and command line tools for processing image-based RNAi screens.

## Introduction

`rnaiutilities` provide a set of python modules and commandline scripts that can be used to process, convert, query and analyse imaged-based RNAi-screens.

The packages are designed for the following workflow:

* Download raw `mat` files from an openBIS instance or where ever your data lie. The `mat` files are supposed to be created by `CellProfiler`, i.e. platewise data-sets, where every file describes a single features for single-cells.

* Parse the downloaded data using `rnai-parse`: install the package, and process as described in the package folder. This generates a list of raw `tsv`s files or a bundled `h5` file. Until now the parser writes featuresets for *cells*, *perinuclei*, *nuclei*, *expandednuclei*,  *bacteria* and *invasomes*.

* Query the meta DB using ``rnai-query`` and create and combine datasets. For that first meta files generated from the step above are written into a database. Then the DB can be queried against to subset single *genes*, *sirnas*, *pathogens*, etc. and write the *normalized* results.

## Installation

Make sure to have `python3` installed. `rnaiutilities` does not support

previous versions. The best way to do that is to download [anaconda](https://www.continuum.io/downloads) and create a

virtual [environment](https://conda.io/docs/using/envs.html).

Download the latest [release](https://github.com/dirmeier/rnaiutilities/releases) first and install it using:

```bash

  pip install .

```

If you get errors, I probably forgot some dependency.

## Documentation

Check out the documentation [here](https://rnaiutilities.readthedocs.io/en/latest/).

## Author

Simon Dirmeier