pertpy 0.11.2__py3-none-any.whl → 0.11.3__py3-none-any.whl

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Files changed (5) hide show
  1. pertpy/__init__.py +1 -1
  2. {pertpy-0.11.2.dist-info → pertpy-0.11.3.dist-info}/METADATA +33 -5
  3. {pertpy-0.11.2.dist-info → pertpy-0.11.3.dist-info}/RECORD +5 -5
  4. {pertpy-0.11.2.dist-info → pertpy-0.11.3.dist-info}/WHEEL +0 -0
  5. {pertpy-0.11.2.dist-info → pertpy-0.11.3.dist-info}/licenses/LICENSE +0 -0
pertpy/__init__.py CHANGED
@@ -2,7 +2,7 @@
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  __author__ = "Lukas Heumos"
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  __email__ = "lukas.heumos@posteo.net"
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- __version__ = "0.11.2"
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+ __version__ = "0.11.3"
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  import warnings
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{pertpy-0.11.2.dist-info → pertpy-0.11.3.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: pertpy
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- Version: 0.11.2
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+ Version: 0.11.3
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  Summary: Perturbation Analysis in the scverse ecosystem.
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  Project-URL: Documentation, https://pertpy.readthedocs.io
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  Project-URL: Source, https://github.com/scverse/pertpy
@@ -132,22 +132,50 @@ You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
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  pip install pertpy
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  ```
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+ ### Differential gene expression
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+
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+ If you want to use the differential gene expression interface, please install pertpy by running:
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+ ```console
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+ pip install 'pertpy[de]'
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+ ```
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+
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+ ### tascCODA
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+
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  if you want to use tascCODA, please install pertpy as follows:
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  ```console
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  pip install 'pertpy[tcoda]'
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  ```
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- If you want to use the differential gene expression interface, please install pertpy by running:
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+ ### milo
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+ milo further requires edger, statmod, and rpy2 to be installed:
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+ ```R
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+ BiocManager::install("edgeR")
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+ BiocManager::install("statmod")
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+ ```
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  ```console
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- pip install 'pertpy[de]'
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+ pip install rpy2
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  ```
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  ## Citation
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- [Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
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- bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)
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+ ```bibtex
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+ @article {Heumos2024.08.04.606516,
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+ author = {Heumos, Lukas and Ji, Yuge and May, Lilly and Green, Tessa and Zhang, Xinyue and Wu, Xichen and Ostner, Johannes and Peidli, Stefan and Schumacher, Antonia and Hrovatin, Karin and Müller, Michaela and Chong, Faye and Sturm, Gregor and Tejada, Alejandro and Dann, Emma and Dong, Mingze and Bahrami, Mojtaba and Gold, Ilan and Rybakov, Sergei and Namsaraeva, Altana and Moinfar, Amir and Zheng, Zihe and Roellin, Eljas and Mekki, Isra and Sander, Chris and Lotfollahi, Mohammad and Schiller, Herbert B. and Theis, Fabian J.},
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+ title = {Pertpy: an end-to-end framework for perturbation analysis},
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+ elocation-id = {2024.08.04.606516},
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+ year = {2024},
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+ doi = {10.1101/2024.08.04.606516},
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+ publisher = {Cold Spring Harbor Laboratory},
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+ URL = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516},
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+ eprint = {https://www.biorxiv.org/content/early/2024/08/07/2024.08.04.606516.full.pdf},
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+ journal = {bioRxiv}
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+ }
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+ ```
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  [pip]: https://pip.pypa.io/
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  [pypi]: https://pypi.org/
{pertpy-0.11.2.dist-info → pertpy-0.11.3.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
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- pertpy/__init__.py,sha256=wwZLpjFSDAZzGA0HGNuk8LoxXjWdrD9OKvpJ4fdsHZU,716
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+ pertpy/__init__.py,sha256=nuIzUydNMtNnhu1E4ffxU9gCgIdLi3liUv7dylR-2_I,716
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  pertpy/_doc.py,sha256=j5TMNC-DA9yIMqIIUNpjpcVgWfRqyBBfvbRjnCM_OLs,427
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  pertpy/_types.py,sha256=IcHCojCUqx8CapibNkcYf2TUqjBFP2ujeELvn_IBSBQ,154
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  pertpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -52,7 +52,7 @@ pertpy/tools/_scgen/_base_components.py,sha256=Qq8myRUm43q9XBrZ9gBggfa2cSV2wbz_K
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  pertpy/tools/_scgen/_scgen.py,sha256=31T8ez0FxABIbunJHCk8xvGulHFb8RHXSsyM_z1WsPY,30850
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  pertpy/tools/_scgen/_scgenvae.py,sha256=bPk4v7EdJc7ROdLuDitHiX_Pvwa7Flw2qHRUwBvjLJY,3889
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  pertpy/tools/_scgen/_utils.py,sha256=qz5QUn_Bvk2NGyYVzp3jgjWTFOMt1YyHwUo6HWtoThY,2871
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- pertpy-0.11.2.dist-info/METADATA,sha256=jlccMD9v37v5vcJJbwpumliEoQR-07sy8vwCKzLL7D0,8047
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- pertpy-0.11.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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- pertpy-0.11.2.dist-info/licenses/LICENSE,sha256=XuiT2hxeRInhquEIBKMZ5M21n5syhDQ4XbABoposIAg,1100
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- pertpy-0.11.2.dist-info/RECORD,,
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+ pertpy-0.11.3.dist-info/METADATA,sha256=PM1yN_AADeouMbFT9X2m4Qv4VfPJ2PFgAbC2FNScIXs,8726
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+ pertpy-0.11.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ pertpy-0.11.3.dist-info/licenses/LICENSE,sha256=XuiT2hxeRInhquEIBKMZ5M21n5syhDQ4XbABoposIAg,1100
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+ pertpy-0.11.3.dist-info/RECORD,,