diff --git a/README.md b/README.md index 073e927..588b380 100644 --- a/README.md +++ b/README.md @@ -12,9 +12,9 @@ LIANA+ is a scalable framework that integrates and extends existing methods and -## Development & Contributions +## Contributions -We welcome suggestions, ideas, and contributions! Please use do not hesitate to contact us, open issues, and check the [contributions guide](https://liana-py.readthedocs.io/en/latest/contributing.html). +We welcome suggestions, ideas, and contributions! Please do not hesitate to contact us, open issues, and check the [contributions guide](https://liana-py.readthedocs.io/en/latest/contributing.html). ## Vignettes A set of extensive vignettes can be found in the [LIANA+ documentation](https://liana-py.readthedocs.io/en/latest/). diff --git a/docs/source/notebooks/basic_usage.ipynb b/docs/source/notebooks/basic_usage.ipynb index d4dcc02..822b7e7 100644 --- a/docs/source/notebooks/basic_usage.ipynb +++ b/docs/source/notebooks/basic_usage.ipynb @@ -1676,9 +1676,11 @@ "\n", "where we take the minimum probability for each interaction across the score vectors, and we apply a Bonferroni multi-testing correction to the P-values by multiplying them by n.\n", "\n", + "\n", "**Notes:**\n", + "\n", "- Δ Some differences are expected with the original implementations largely due to different preprocessing steps which LIANA+ harmonised across the different methods. Specifically, LIANA+ considers the minimum score (e.g. average expression) for complex subunits, while some methods consider the mean, geometric mean, or simply do not account for complexes at all.\n", - "- † The original [CellChat](https://github.com/jinworks/CellChat) implementation additionally uses information about mediator proteins and pathways, which are specific to the CellChat resource. Since we wish to keep LIANA+ resource-agnostic, **we do not utilise mediator information**, as such while the remainder of the score calculation is identical to CellChat's LR probabilities, some differences are anticipated.\n", + "- † The original [CellChat](https://github.com/jinworks/CellChat) implementation additionally uses information about mediator proteins and pathways, which are specific to the CellChat resource. Since we wish to keep LIANA+ resource-agnostic, **we do not utilise mediator information**, as such while the remainder of the score calculation is identical to CellChat's LR probabilities, some differences are anticipated.\n", "- Ѫ While we refer to the genes as ligands and receptors for simplicity, these can represent the gene expression also of membrane-bound or extracellular-matrix proteins, as well as heteromeric complexes for which the minimum expression across subunits is used.\n", "- ‡ 1-vs-rest cell group log2FC for each gene is calculated as $$log2FC = \\log_2\\left(\\text{mean}(X_i)\\right) - \\log_2\\left(\\text{mean}(X_{\\text{not}_i})\\right)$$\n", "- (*) LIANA considers interactions as occurring only if both the ligand and receptor, as well as all of their subunits, are expressed above a certain proportion of cells in both clusters involved in the interaction (0.1 by default). This can be formulated as an indicator function as follows:\n", @@ -1690,7 +1692,7 @@ "metadata": {}, "source": [ "\n", - "### 🙏 Please consider citing the original methods when using their LIANA+ re-implementations in your work! 🙏 \n", + "### 🙏 Please consider citing the original methods when using their LIANA+ adaptations in your work! 🙏 \n", "\n", "*While LIANA+ simply aims to ease ligand-receptor inference, the original authors and developers should be credited for their work.*\n", "\n",