Skip to content

Commit

Permalink
add date to news and news to readme
Browse files Browse the repository at this point in the history
  • Loading branch information
dbdimitrov committed Jul 4, 2022
1 parent e120a4d commit efb1249
Show file tree
Hide file tree
Showing 3 changed files with 19 additions and 13 deletions.
2 changes: 1 addition & 1 deletion NEWS.md
Original file line number Diff line number Diff line change
@@ -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
Expand Down
28 changes: 17 additions & 11 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,15 +3,6 @@
<!-- badges: end -->

# LIANA: a LIgand-receptor ANalysis frAmework <img src="https://www.dropbox.com/s/z6s7cp00kbbm1s9/liana_logo.png?raw=1" align="right" height="100">

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}
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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

<strong> 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! </strong>


### 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)
Expand Down
2 changes: 1 addition & 1 deletion vignettes/liana_ortho.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down

0 comments on commit efb1249

Please sign in to comment.