From efb1249af46f576d1d620956053cfa93b2cee961 Mon Sep 17 00:00:00 2001 From: dbdimitrov Date: Mon, 4 Jul 2022 17:12:23 +0200 Subject: [PATCH] add date to news and news to readme --- NEWS.md | 2 +- README.md | 28 +++++++++++++++++----------- vignettes/liana_ortho.Rmd | 2 +- 3 files changed, 19 insertions(+), 13 deletions(-) diff --git a/NEWS.md b/NEWS.md index e0725e39..1b00e4ea 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# LIANA 0.1.5 (XX.07.22) +# LIANA 0.1.5 (04.07.22) ## Changes - Re-implemented the `RRA` method from Kolde et al., 2012, as a consequence of diff --git a/README.md b/README.md index 576d6c8d..a9045ca8 100644 --- a/README.md +++ b/README.md @@ -3,15 +3,6 @@ # LIANA: a LIgand-receptor ANalysis frAmework - -The continuous developments of single-cell RNA-Seq (scRNA-Seq) have sparked -an immense interest in understanding intercellular crosstalk. Multiple -tools and resources that aid the investigation of cell-cell communication (CCC) -were published recently. -However, these methods and resources are usually in a fixed combination of a -tool and its corresponding resource, but in principle any resource could be -combined with any method. - ## Install LIANA ```{r} @@ -44,7 +35,16 @@ Additional tutorials: ## LIANA Framework - + +The continuous developments of single-cell RNA-Seq (scRNA-Seq) have sparked +an immense interest in understanding intercellular crosstalk. Multiple +tools and resources that aid the investigation of cell-cell communication (CCC) +were published recently. +However, these methods and resources are usually in a fixed combination of a +tool and its corresponding resource, but in principle any resource could be +combined with any method. + + To this end, we built a framework to decouple the methods from their corresponding resources. LIANA also goes a step further as it provides: @@ -128,13 +128,19 @@ as well as to explore custom filter options see [customizing OmniPath resources] If you are interested in making use of the LIANA architecture for your own method, [this vignette](https://saezlab.github.io/liana/articles/liana_devel.html) provides instructions how to obtain a comprehensive table of LR statistics, which can then be used by custom scoring functions. In the [same vignette](https://saezlab.github.io/liana/articles/liana_devel.html) are also instructions how to install and run the original methods via a convenient R wrapper, e.g. for their benchmark. - + ## Contact We appreciate any feedback, so please do not hesitate to open an issue on the [liana github page](https://github.com/saezlab/liana)! +## NEWS + + We are commited to the further developments of LIANA and we refer the users to +check the [NEWS](https://github.com/saezlab/liana/blob/master/NEWS.md) page after very update! + + ### Citing `LIANA`: Dimitrov, D., Türei, D., Garrido-Rodriguez M., Burmedi P.L., Nagai, J.S., Boys, C., Flores, R.O.R., Kim, H., Szalai, B., Costa, I.G., Valdeolivas, A., Dugourd, A. and Saez-Rodriguez, J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. *Nat Commun 13*, 3224 (2022). [https://doi.org/10.1038/s41467-022-30755-0](https://www.nature.com/articles/s41467-022-30755-0) diff --git a/vignettes/liana_ortho.Rmd b/vignettes/liana_ortho.Rmd index b24b9fc1..616869c8 100644 --- a/vignettes/liana_ortho.Rmd +++ b/vignettes/liana_ortho.Rmd @@ -116,7 +116,7 @@ documentation for more information. -## ## Generating an External Dictionary +## Generating an External Dictionary In order to convert a human resource to any other organism, we need a dictionary which maps human gene symbols to their orthologs from another species, which might not be available via OmniPath.