Metadata-Version: 2.4
Name: spectrseqtools
Version: 0.2.1
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Rust
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Dist: polars>=1.9.0,<2.0
Requires-Dist: pulp>=2.3.0,<3.0
Requires-Dist: ddargparse>=0.3.0,<0.4
Requires-Dist: typed-argument-parser>=1.10.1,<2.0
Requires-Dist: altair>=5.4.1,<6.0
Requires-Dist: pyyaml>=6.0.2,<7.0
Requires-Dist: loguru>=0.7.2,<0.8
Requires-Dist: numpy>=2.2.3,<3.0
Requires-Dist: platformdirs>=4.3.8,<5.0
Requires-Dist: clr-loader>=0.2.7.post0,<0.3
Requires-Dist: ms-deisotope>=0.0.60,<0.1
Requires-Dist: pythonnet>=3.0.5,<4.0
Requires-Dist: tqdm>=4.67.1,<5.0
Requires-Dist: scikit-learn>=1.7.2,<2.0
Requires-Dist: dbscan1d>=0.2.3,<0.3
License-File: LICENSE
Summary: SpectrSeqTools is a fully automatic analysis platform for sequencing small RNA molecules including 144 known post translational modifications measured via LC-MS/MS data.
Author-email: Laura Christine Kuehle <laura.kuehle@mpi-dortmund.mpg.de>, Juan Antonio Magalang <juan.magalang@mpi-dortmund.mpg.de>, Moshir Harsh <btemoshir@gmail.com>, Johannes Koester <johannes.koester@uni-due.de>
License-Expression: GPL-3.0-only
Requires-Python: >=3.12, <3.14
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
Project-URL: Homepage, https://github.com/spectrseq/spectrseqtools

# SpectrSeqTools

SpectrSeqTools is a fully automatic analysis platform for sequencing small RNA molecules including 144 known post translational modifications measured via LC-MS/MS data.

## Installation

We recommend installing SpectrSeqTools via the pixi package manager:

```bash
pixi global install -c conda-forge -c bioconda spectrseqtools
```

Alternatively, a conda environment (for use with e.g. Snakemake) can de defined as follows

```yaml
channels:
  - conda-forge
  - bioconda
  - nodefaults
dependencies:
  - spectrseqtools
```
For reproducibility, make sure to specify the version you want to use next to the package name above.

## Usage

After installing, run

```bash
spectrseqtools --help
```

to get help using SpectrSeqTools.
More extensive documentation with examples will appear here soon.

