update doc

Author: kullrich

docs/environment.yml

@@ -17,7 +17,7 @@ dependencies:
   - scipy>=1.15.1
   - seaborn>=0.13.2
   - setuptools>=67.6.0
-  - statannot>=0.2.3
+  - statannotations>=0.7.1
   - pip:
       - harmonypy>=0.0.10
       - leidenalg>=0.10.2

docs/references/index.rst

@@ -17,6 +17,9 @@ Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D.M., Hill, A.J., Zhang, F.
 Steemers, F.J. and Trapnell, C. (2019). **The single-cell transcriptional landscape of mammalian organogenesis.**
 *Nature*, **566(7745)**. `https://doi.org/10.1038/s41586-019-0969-x <https://doi.org/10.1038/s41586-019-0969-x>`_
 
+Charlier, F., Weber, M., Izak, D., Harkin, E., Magnus, M., Lalli, J., Fresnais, L., Chan, M., Markov, N., Amsalem, O.,
+Proost, S., Krasoulis, A., and Repplinger, S. (2022). **Statannotations (v0.7.1).** *Zenodo*. `<https://doi.org/10.5281/zenodo.7213391 https://doi.org/10.5281/zenodo.7213391>`_
+
 Cheng, S., Pei, Y., He, L., Peng, G., Reinius, B., Tam, P.P., Jing, N. and Deng, Q. (2019). **Single-cell RNA-seq
 reveals cellular heterogeneity of pluripotency transition and X chromosome dynamics during early mouse development.**
 *Cell reports*, **26(10)**. `https://doi.org/10.1016/j.celrep.2019.02.031 <https://doi.org/10.1016/j.celrep.2019.02.031>`_

docs/requirements.txt

@@ -17,7 +17,7 @@ seaborn>=0.13.2
 setuptools>=67.6.0
 sphinx<8.2.0,>=7.2.6
 sphinx-rtd-theme>=1.3.0
-statannot>=0.2.3
+statannotations>=0.7.1
 taxadb2>=0.12.3
 umap-learn>=0.5.7
 wget>=3.2

docs/tutorials/orthofinder.rst

@@ -10,6 +10,12 @@ Step 0 - run OrthoFinder
    - `SonicParanoid2 <https://gitlab.com/salvo981/sonicparanoid2>`_
    - `Broccoli <https://github.com/rderelle/Broccoli>`_
 
+   and the following databases:
+
+   - `EggNOG v6.0 <http://eggnog6.embl.de/>`_
+   - `PLAZA <https://bioinformatics.psb.ugent.be/plaza/>`_
+   - `OrthoMCL <https://orthomcl.org/orthomcl/app>`_
+
 In order to extract an orthomap from `OrthoFinder <https:https://github.com/davidemms/OrthoFinder>`_ results, one needs to run `OrthoFinder <https:https://github.com/davidemms/OrthoFinder>`_.
 
 Mandatory OrthoFinder results files

environment.yml

@@ -16,7 +16,7 @@ dependencies:
   - scipy>=1.15.1
   - seaborn>=0.13.2
   - setuptools>=67.6.0
-  - statannot>=0.2.3
+  - statannotations>=0.7.1
   - pip:
       - harmonypy>=0.0.10
       - leidenalg>=0.10.2

pyproject.toml

@@ -46,7 +46,7 @@ dependencies = [
     "scipy>=1.15.1",
     "seaborn>=0.13.2",
     "setuptools>=67.6.0",
-    "statannot>=0.2.3",
+    "statannotations>=0.7.1",
     "taxadb2>=0.12.3",
     "umap-learn>=0.5.7",
     "wget>=3.2"