Metadata-Version: 2.1
Name: picked-group-fdr
Version: 0.1.0
Summary: Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments
Home-page: https://github.com/kusterlab/picked_group_fdr
License: Apache-2.0
Keywords: mass spectrometry,protein inference,proteomics
Author: Matthew The
Author-email: matthew.the@tum.de
Requires-Python: >=3.6.9,<4.0.0
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Dist: cython (>=0.29.21,<0.30.0)
Requires-Dist: dataclasses (>=0.8,<0.9)
Requires-Dist: llvmlite (==0.31.0)
Requires-Dist: matplotlib (>=3.3.1,<4.0.0)
Requires-Dist: mokapot (>=0.3,<0.4)
Requires-Dist: networkx (>=2.4,<3.0)
Requires-Dist: numpy (>=1.18,<2.0)
Requires-Dist: triqler (>=0.4.0,<0.5.0)
Project-URL: Repository, https://github.com/kusterlab/picked_group_fdr
Description-Content-Type: text/markdown

# Picked Protein Group FDR

Scalable, accurate and sensitive protein group FDRs for large-scale mass spectrometry experiments

## Running Picked Protein Group FDR using the GUI

On Windows, you can download the `PickedGroupFDR_GUI_windows.zip` from the latest release, unzip it and open `PickedGroupFDR.exe` to start the GUI (no installation necessary).

Alternatively, on all platforms, first install Picked Protein Group FDR as explained below. Then install `PyQt5` (`pip install PyQt5`) and run:

```shell
python gui.py
```

## Running Picked Protein Group FDR from the command line

First install Picked Protein Group FDR as explained below, then run:

```shell
python -m picked_group_fdr --mq_evidence </path/to/mq_evidence_txt> --fasta </path/to/fasta_file>
```

## Installation

Picked Protein Group FDR is available on PyPI and can be installed with `pip`:

```shell
pip install picked_group_fdr
```

Alternatively, you can install directly from this repository:

```shell
git clone https://github.com/kusterlab/picked_group_fdr.git
pip install .
```

