semvec/pypi-packages huggingface dataset:
MSanalyst 0.1.2
A tool for molecular networking and annotation
Requires Python: >=3.8

# MSanalyst
This repository contains the original source code of MSanalyst
![MSanalystlogo](MSanalyst_logo.jpg)

# Installation
## pip version
```bash
pip install msanalyst
```
## docker version
```bash
docker pull
```


# Quick start
## Preprocess
Before applying MSanalyst, raw mass spectrometry (MS) data should be converted using [MSconvert](https://mzmine.github.io/mzmine_documentation/data_conversion.html). 
It is recommended to use [MZmine-based untargeted LC-MS workflow](https://mzmine.github.io/mzmine_documentation/workflows/lcmsworkflow/lcms-workflow.html) 
to generate the `quant.csv` and `mgf` files as inputs. 

## Module usage
Here we briefly introduce the command of MSanalyst quick start:
Using `-h` for help messages in MSanalyst: 

- `main.py` 
for Default analysis workflow of MSanalyst.

```bash
python main.py  -q ./example/example_quant.csv -m ./example/example.mgf -o ./example/
```

- `re-networking.py` for quick re-analysis of the results generated by `main.py` command.

```bash
python re-networking.py -m ./example/example.mgf -q ./example/example_quant.csv -scm neutral_loss -scs 0.5 -scp 4
```

- `ms1search.py`
for single quick ms<sup>1</sup> searching

```bash
python ms1search.py -qms1 227.234
```

- `ms2search.py` 
for single ms<sup>2</sup> searching

```bash
python ms2search.py -m single.mgf
```

- `customized_db.py` 
for generating customized mass spectrometry database

```bash
python customized_db.py -m ./customed_db/Xiamenmycins.mgf -li ./customed_db/Xiamenmycins.xlsx 
```

- `mn_merging.py`
for merging different molecular netowrks

```bash
python mn_merging.py -mn1 ./example/example_quant_result/example_modified_cosine_0.7_5.graphml -mn2 ./example/example_quant_result/example_modified_cosine_0.1_1.graphml -o ./example/
```

## Documentation
Please see the following links for detailed instructions, parameter usage and more information.
- [Online documentation](https://msanalyst.net/a/about) 
- [Video tutorials](https://msanalyst.net/a/about)
- [MSanalyst library](https://drive.google.com/file/d/1w6HF3w1KIJlTz_QaVqqtN1BzkGDhDgzw/view)