Metadata-Version: 2.1
Name: scbs
Version: 0.6.0
Summary: command line tool for the analysis of single-cell bisulfite-sequencing data
Home-page: https://github.com/LKremer/scbs
License: GPL-3.0-or-later
Keywords: biology,bioinformatics,single cell,methylation,single cell bisulfite sequencing
Author: Lukas PM Kremer
Author-email: L-Kremer@web.de
Maintainer: Lukas PM Kremer
Maintainer-email: L-Kremer@web.de
Requires-Python: >=3.8,<3.11
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Dist: click (>=7.1.2,<8.1)
Requires-Dist: click-help-colors (>=0.9,<1)
Requires-Dist: colorama (>=0.3.9,<1)
Requires-Dist: numba (>=0.53.0,<1)
Requires-Dist: numpy (>=1.20.1,<2)
Requires-Dist: pandas (>=1.2.3,<2)
Requires-Dist: scipy (>=1.6.1,<2)
Requires-Dist: statsmodels (>=0.12.2,<1)
Project-URL: Repository, https://github.com/LKremer/scbs
Description-Content-Type: text/markdown

# `scbs`: A Command Line Tool for the Analysis of Single-Cell Bisulfite-Sequencing Data

## Installation

You can install `scbs` from the Python package index as follows:
```
python3 -m pip install --upgrade pip  # you need a recent pip version
python3 -m pip install scbs
```
Then restart your terminal. The installation is now finished and the command line interface should now be available when typing the command `scbs` in your terminal.
If this is not the case, check the "troubleshooting" section below.  


## Updating to the latest version
Just use `--upgrade` when installing the package, otherwise it's the same process as installing:
```
python3 -m pip install --upgrade scbs
```
Afterwards, make sure that the latest version is correctly installed:
```
scbs --version
```

## [Tutorial](docs/tutorial.md) of a typical `scbs` run
A tutorial can be found [here](docs/tutorial.md).

Also make sure to read the help by typing `scbs --help` or by checking [this page](docs/commands.md).


## What can this package do?

`scbs` takes as input a number of single-cell methylation files and allows you to quickly and easily obtain a cell × region matrix for downstream analysis.
It also facilitates quality control, allows you to discover variably methylated regions (VMRs), accurately quantifies methylation in genomic intervals, and stores your sc-methylomes in an efficient manner.

![schematic showing the capabilities of scbs](docs/Fig_workflow.png)

You can find a list of the available `scbs` commands [here](docs/commands.md).


## bioRxiv preprint

For a detailed explanation of the methods implemented in `scbs`, please check our bioRxiv preprint:

*Analyzing single-cell bisulfite sequencing data with scbs*  
Lukas PM Kremer, Leonie Kuechenhoff, Santiago Cerrizuela, Ana Martin-Villalba, Simon Anders  
bioRxiv 2022.06.15.496318; doi: [https://doi.org/10.1101/2022.06.15.496318](https://doi.org/10.1101/2022.06.15.496318)



## Troubleshooting

#### Installation issues

Carefully check the output log of PIP. Look for a message like `WARNING: The script scbs is installed in '/home/ubuntu/.local/bin' which is not on PATH.`, which would indicate that you need to add `/home/ubuntu/.local/bin` to your path. Alternatively, you can copy `/home/ubuntu/.local/bin/scbs` to e.g. `/usr/local/bin`.

If you encounter other problems during installation, make sure you have Python3.8 or higher, and make sure you have the latest PIP version. If the problem persists, consider installing `scbs` in a clean Python environment (for example using [venv](https://docs.python.org/3/library/venv.html)).

#### Too many open files
If you encounter a "too many open files" error during `scbs prepare` (`OSError: [Errno 24] Too many open files`), you need to increase the maximum number of files that can be opened. In Unix systems, try `ulimit -n 9999`.



## Contributors
- [Lukas PM Kremer](https://github.com/LKremer)
- [Martina Braun](https://github.com/martinabraun)
- [Leonie Küchenhoff](https://github.com/LeonieKuechenhoff)
- [Alexey Uvarovskii](https://github.com/alexey0308)
- [Simon Anders](https://github.com/simon-anders)

