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24 changes: 13 additions & 11 deletions README.md
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Expand Up @@ -137,18 +137,20 @@ regarding documentations!

## References

If you are cytomulating in your workflow, citing [our paper](https://doi.org/10.1101/2022.06.14.496200) is appreciated:
If you are cytomulating in your workflow, citing [our paper](https://doi.org/10.1186/s13059-023-03099-1) is appreciated:

```
@article {Yang2022.06.14.496200,
author = {Yang, Yuqiu and Wang, Kaiwen and Lu, Zeyu and Wang, Tao and Wang, Xinlei},
title = {Cytomulate: Accurate and Efficient Simulation of CyTOF data},
elocation-id = {2022.06.14.496200},
year = {2022},
doi = {10.1101/2022.06.14.496200},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200},
eprint = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200.full.pdf},
journal = {bioRxiv}
@article{Yang2023,
title = {Cytomulate: accurate and efficient simulation of CyTOF data},
volume = {24},
ISSN = {1474-760X},
url = {http://dx.doi.org/10.1186/s13059-023-03099-1},
DOI = {10.1186/s13059-023-03099-1},
number = {1},
journal = {Genome Biology},
publisher = {Springer Science and Business Media LLC},
author = {Yang, Yuqiu and Wang, Kaiwen and Lu, Zeyu and Wang, Tao and Wang, Xinlei},
year = {2023},
month = nov
}
```
2 changes: 1 addition & 1 deletion cytomulate/__init__.py
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Expand Up @@ -5,7 +5,7 @@
"""

__version__ = "0.1.1"
__author__ = "Yuqiu Yang, Kevin Wang, Tao Wang, Sherry Wang"
__author__ = "Yuqiu Yang, Kevin Wang, Zeyu Lu, Tao Wang, Sherry Wang"

from cytomulate.creation.cytof_data import CreationCytofData
from cytomulate.emulation.cytof_data import EmulationCytofData
8 changes: 4 additions & 4 deletions docs/source/index.rst
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Expand Up @@ -68,8 +68,8 @@ For more details, **read our tutorials and documentations linked below!** Or try
:hidden:

references
Our Paper <https://doi.org/10.1101/2022.04.26.489549>
Dr. Xinlei (Shery) Wang <https://people.smu.edu/swang/>
Our Paper <https://doi.org/10.1186/s13059-023-03099-1>
Dr. Xinlei (Sherry) Wang <https://www.uta.edu/academics/faculty/profile?username=wangx9>
Dr. Tao Wang <https://qbrc.swmed.edu/labs/wanglab/aboutpi.php>
DBAI <https://dbai.biohpc.swmed.edu/>
GitHub <https://github.com/kevin931/cytomulate/>
Expand All @@ -79,11 +79,11 @@ For more details, **read our tutorials and documentations linked below!** Or try
Resources
***********************

For our paper, read our preprint `here <https://doi.org/10.1101/2022.04.26.489549>`_.
For our paper, read our preprint `here <https://doi.org/10.1186/s13059-023-03099-1>`_.

For more resources on our labs, collaborators, and related projects, please visit the following:

* `Dr. Xinlei (Shery) Wang faculty page <https://people.smu.edu/swang/>`_
* `Dr. Xinlei (Sherry) Wang faculty page <https://www.uta.edu/academics/faculty/profile?username=wangx9>`_
* `Dr. Tao Wang Lab <https://qbrc.swmed.edu/labs/wanglab/aboutpi.php>`_
* `Database for Actionable Immunology (DBAI) for more computational immunology-related tools <https://dbai.biohpc.swmed.edu/>`_

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24 changes: 13 additions & 11 deletions docs/source/references.rst
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Expand Up @@ -3,7 +3,7 @@ References
################

Here, you will find a list of relevant references. For a complete list, you can
read `our paper <https://doi.org/10.1101/2022.04.26.489549>`_.
read `our paper <https://doi.org/10.1186/s13059-023-03099-1>`_.

-----------------------

Expand All @@ -15,16 +15,18 @@ If you decide to cytomulate it in your package, citing our paper is highly appre

.. code-block:: text
@article {Yang2022.06.14.496200,
author = {Yang, Yuqiu and Wang, Kaiwen and Lu, Zeyu and Wang, Tao and Wang, Xinlei},
title = {Cytomulate: Accurate and Efficient Simulation of CyTOF data},
elocation-id = {2022.06.14.496200},
year = {2022},
doi = {10.1101/2022.06.14.496200},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200},
eprint = {https://www.biorxiv.org/content/early/2022/06/16/2022.06.14.496200.full.pdf},
journal = {bioRxiv}
@article{Yang2023,
title = {Cytomulate: accurate and efficient simulation of CyTOF data},
volume = {24},
ISSN = {1474-760X},
url = {http://dx.doi.org/10.1186/s13059-023-03099-1},
DOI = {10.1186/s13059-023-03099-1},
number = {1},
journal = {Genome Biology},
publisher = {Springer Science and Business Media LLC},
author = {Yang, Yuqiu and Wang, Kaiwen and Lu, Zeyu and Wang, Tao and Wang, Xinlei},
year = {2023},
month = nov
}
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4 changes: 2 additions & 2 deletions setup.py
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Expand Up @@ -58,8 +58,8 @@ def run(self):
name = "cytomulate",
version = VERSION,
description = "Accurate and Efficient Simulation of CyTOF data",
author = "Yuqiu Yang, Kevin Wang, Tao Wang, Sherry Wang",
author_email = "[email protected], [email protected], [email protected], swang@smu.edu",
author = "Yuqiu Yang, Kevin Wang, Zeyu Lu, Tao Wang, Sherry Wang",
author_email = "[email protected], [email protected], [email protected], [email protected], xinlei.wang@uta.edu",
long_description_content_type = "text/markdown",
long_description = open("README.md").read(),
packages=["cytomulate",
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