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Merged
MayraRuizT merged 8 commits into from
Oct 6, 2026
Merged

Update dev branch with new tutorial #48

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07fc572
Merge pull request #47 from CostaLab/dev
MayraRuizT Sep 9, 2026
e555a69
avoid plotting nw stats twice in tutorials
MayraRuizT Sep 9, 2026
f03a7b1
Update README and documentation adding new zenodo link and new PICseq…
MayraRuizT Sep 10, 2026
07fc138
bump version to 1.1.0
MayraRuizT Sep 10, 2026
fef12bb
remove old poetry lock file
MayraRuizT Sep 10, 2026
a178b93
bump version in docs conf.py
MayraRuizT Sep 10, 2026
4907789
update pypi badge
MayraRuizT Sep 10, 2026
d85c524
add references and tutorial links
jmichellejm Sep 24, 2026
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4 changes: 2 additions & 2 deletions README.md
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# NicheSphere

[![DOI](https://zenodo.org/badge/685916590.svg)](https://doi.org/10.5281/zenodo.18756710)
![PyPI - Version](https://img.shields.io/pypi/v/NicheSphere)
[![PyPI version](https://img.shields.io/pypi/v/NicheSphere.svg)](https://pypi.org/project/NicheSphere/)


NicheSphere is an sc-verse compatible Python library which allows the user to find differential co-localization domains / niches based on cell type pair co-localization probabilities in different conditions. Cell type pair co-localization probabilities can be obtained in different ways, for example, through deconvolution of spatial transcriptomics / PIC-seq data (getting the probabilities of finding each cell type in each spot / multiplet) ; or counting nearest neighbors of each type for each cell in single cell spatial data like MERFISH or CODEX.

It also offers the possibility to look at biological process based differential communication between cell type pairs or differential co-localization domains based on Ligand-Receptor pairs expression data, which can be obtained from diverse cell cell communication tools, such as [CrossTalkeR](https://costalab.github.io/CrossTalkeR/).

You can find our documentation and an application example on the Myocardial Infarction atlas data from Kuppe et. al. 2022 here: https://nichesphere.readthedocs.io/en/latest/ , The data you'll need to run the tutorials is stored in [Zenodo](https://doi.org/10.5281/zenodo.15790389)
You can find our documentation and an application example on the Myocardial Infarction atlas data from Kuppe et. al. 2022 here: https://nichesphere.readthedocs.io/en/latest/ , The data you'll need to run the tutorials is stored in [Zenodo](https://doi.org/10.5281/zenodo.22678370)


4 changes: 2 additions & 2 deletions docs/api.rst
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API Reference
=============
API
=====

.. include:: coloc.rst
.. include:: comm.rst
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6 changes: 5 additions & 1 deletion docs/conf.py
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project = 'NicheSphere'
copyright = '2025, Mayra Ruiz, James Nagai'
author = 'Mayra Ruiz, James Nagai'
release = '1.0.2'
release = '1.1.0'

# -- General configuration ---------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
Expand All @@ -41,7 +41,11 @@

# -- BibTeX citation settings
bibtex_bibfiles = ['references.bib']
#bibtex_default_style = 'unsrt'
bibtex_default_style = 'alpha'
bibtex_reference_style = 'author_year'



# -- It hides the input/output prompt numbers (In [1]: / Out [1]:).
nbsphinx_prolog = """
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7 changes: 5 additions & 2 deletions docs/index.rst
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Expand Up @@ -34,6 +34,7 @@ co-localization domains based on Ligand-Receptor pairs expression data, such as
installation
tutorials
api
references

Installation
------------
Expand All @@ -46,7 +47,7 @@ Installation
Citation
--------

If you use ``NicheSphere`` in your research, please cite our paper:
If you use ``NicheSphere`` in your research, please cite our paper :cite:p:`gleitz_nichesphere_2026`:

**NicheSphere reveals Spp1⁺ macrophages as central hubs coordinating fibrotic remodeling in myeloproliferative neoplasms**

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* :doc:`NicheSphere tutorial — Myocardial Infarction (Visium) </notebooks/Nichesphere_tutorial_MIvisium>`
* :doc:`NicheSphere × PILOT: niche-based trajectory inference </notebooks/Nichesphere_tutorial_MIvisium_PILOT>`
* :doc:`NicheSphere PIC-seq tutorial </notebooks/Nichesphere_tutorial_BM_PICseq>`
* :doc:`NicheSphere x PILOT CODEX tutorial </notebooks/Nichesphere_tutorial_CODEX_PILOT>`



Expand All @@ -83,7 +86,7 @@ Docker image and summarized analysis tutorial

We provide access to a Docker image, available at: https://gitlab.com/sysbiobig/ismb-eccb-2025-tutorial-vt3/container_registry.
The Docker image comes preconfigured with all necessary libraries, tools, and software required to follow the hands-on exercises.
Additionally, the repository at https://gitlab.com/sysbiobig/ismb-eccb-2025-tutorial-vt3 contains a summarized Nichesphere
Additionally, the repository at https://gitlab.com/sysbiobig/ismb-eccb-2025-tutorial-vt3 contains a summarized NicheSphere
co-localization + communication analysis tutorial.

API Reference
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