semvec/pypi-packages huggingface dataset:
trackc 0.0.14
Track view of chromosome conformation and multi-omics data
License: MIT
Requires Python: >=3.9

.. image:: https://zenodo.org/badge/572302042.svg
   :target: https://zenodo.org/badge/latestdoi/572302042


=======
trackc
=======

Track view of chromosome conformation and multi-omics data
===========================================================
**trackc** is a python package to flexible visualization of 3D genome and multi-omics data.
It builds on top of `matplotlib`, from which it allow for flexible adjustments.

Trackc's key applications
--------------------------
- Mark the abnormal interaction formed by the structural variation of the genome.
- Show the 3Dgenome interaction and multi-omics data after rearrangement.
- Flexible and convenient layout for multi-track 

Available track types
---------------------
- multi Hi-C heatmap
- Virtual4C
- bigwig signal
- bed position, ChIP-seq or ATAC-seq peaks, TAD domains, SVs
- mark region on heatmap
- zoomin
- gene
- links, interaction loops
- scalebar

Here is an example of du_dynamic_2022 article diagram implemented by trackc.

Installation
============
**PyPI**

Install trackc by running:

.. code-block:: bash

    pip install trackc

**Development version**

To install trackc from GitHub, run::

    pip install git+https://github.com/seqyuan/trackc@main

Documentation
=============
Our documentation provide the full list of possible track types and gallary guidelines for users.

Extensive documentations are available at https://trackc.readthedocs.io


Citation
========
If you use trackc in your analysis, Please cite trackc as follows:

**trackc: a package for flexible visualization of rearrangement 3D genome and multi-omics data**
nbfixme 0.0.1
Utility to fix basic notebook validation errors
License: MIT
Requires Python: >=3.8
Keywords: jupyter,nbformat,notebook,utility,validation

# Utility to fix basic notebook validation errors

This project offers a command line tool to fix jupyter notebook files that have some type of validation errors.
These errors may happen when editing a notebook in non standard jupyter clients like PyCharm or other editors
and they can stop the notebook from being properly processed or displayed in github for example.

Currently the script only deals with one type of error that appears as
`NotebookValidationError: 'execution_count' is a required property`.
This error usually happens when a notebook is saved and its last cell has not been executed.
As a fix the script will add a key `execution_count` with a value of `null` to the cell data
if the key is not already present.

By default the script will change the files in place when there is a fix, but you can specify an OUTDIR
parameter if you prefer to save output files in a different directory.

## Usage

```console
Usage: nbfixme [OPTIONS] [PATH]...

  Utility to fix basic notebook validation errors

  PATH is the path to a notebook file or a
  directory containing *.ipynb files.

  By default the script will change the files in
  place when there is a fix, but you can specify
  an OUTDIR parameter if you prefer to save output
  files in a different directory.

Options:
  -o, --outdir OUTDIR  Save output in directory.
  -c, --check-only     Only check for errors.
  -r, --recurse        Recurse to sub directories.
```

## Example

```console
❯ nbfixme extras -o output
extras/notebook-valid.ipynb ok
extras/notebook-broken.ipynb error
extras/notebook-tofix.ipynb fixed
```

## Installation

You can install the latest version of this module with `pip` or `pipx`

```console
pip install git+ssh://git@github.com/furechan/nbfixme.git
```

## Related Resources
-[The Jupyter Notebook Format](https://nbformat.readthedocs.io/en/latest/)
diff 2023.12.6
You diff objects, you find out why they ain't the same.
License: MIT
Requires Python: >=3.10
Keywords: diff,difference,protocol

====
diff
====

|PyPI| |Pythons| |CI| |pre-commit|

.. |PyPI| image:: https://img.shields.io/pypi/v/diff.svg
  :alt: PyPI version
  :target: https://pypi.org/project/diff/

.. |Pythons| image:: https://img.shields.io/pypi/pyversions/diff.svg
  :alt: Supported Python versions
  :target: https://pypi.org/project/diff/

.. |CI| image:: https://github.com/Julian/diff/workflows/CI/badge.svg
  :alt: Build status
  :target: https://github.com/Julian/diff/actions?query=workflow%3ACI

.. |pre-commit| image:: https://results.pre-commit.ci/badge/github/Julian/diff/main.svg
  :alt: pre-commit.ci status
  :target: https://results.pre-commit.ci/latest/github/Julian/diff/main


``diff`` defines a difference protocol. Watch:

.. code-block:: python

    >>> class LonelyObject:
    ...     def __diff__(self, other):
    ...         return f"{self} is not like {other}"
    ...
    ...     def __repr__(self):
    ...         return "<LonelyObject>"

    >>> from diff import diff
    >>> diff(LonelyObject(), 12).explain()
    '<LonelyObject> is not like 12'