From 1bd880d1257d6e2a1fffe86bf0040c0a5b60c051 Mon Sep 17 00:00:00 2001 From: enblacar Date: Fri, 26 Jul 2024 16:37:59 +0200 Subject: [PATCH 1/2] Enabled syntax highlight for R code in README.md and added liana.Rproj to .gitignore to match the current repository name. --- .gitignore | 1 + README.md | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 6ca8ff4c..077ec860 100644 --- a/.gitignore +++ b/.gitignore @@ -15,4 +15,5 @@ inst/cytosig_signature_centroid.csv .Rhistory LIANA.Rproj .gitattributes +liana.Rproj diff --git a/README.md b/README.md index 9609af32..79440f98 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ LIANA enables the use of any combination of ligand-receptor methods and resources, and their consensus. A faster and memory efficient Python implementation is available [here](https://github.com/saezlab/liana-py). ## Install LIANA -```{r} +```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") From 63fa793152c7aa694b852e196d04955a70eac07d Mon Sep 17 00:00:00 2001 From: enblacar Date: Fri, 26 Jul 2024 16:53:40 +0200 Subject: [PATCH 2/2] Fixed broken link in SCpubr's reference in liana_tutorial.Rmd. --- vignettes/liana_tutorial.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/liana_tutorial.Rmd b/vignettes/liana_tutorial.Rmd index e2bd29ce..fafb2972 100644 --- a/vignettes/liana_tutorial.Rmd +++ b/vignettes/liana_tutorial.Rmd @@ -208,7 +208,7 @@ p <- chord_freq(liana_trunc, ``` -For more advanced visualization options, we kindly refer the user to [SCPubr](https://enblacar.github.io/SCpubr-book/21-LigandReceptorPlot.html). +For more advanced visualization options, we kindly refer the user to [SCpubr](https://github.com/enblacar/SCpubr/) (see [`SCpubr::do_LigandReceptorPlot()`](https://enblacar.github.io/SCpubr-book-v1/21-LigandReceptorPlot.html)). ## Run any method of choice.