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minor improvemtns to docs, remove non-standard symbols
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dbdimitrov committed Aug 6, 2024
1 parent 44ba0a3 commit ef77588
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Package: liana
Type: Package
Title: LIANA: a LIgand-receptor ANalysis frAmework
Version: 0.1.13
Version: 0.1.14
Authors@R: c(
person(
given = "Daniel",
Expand All @@ -19,7 +19,7 @@ Authors@R: c(
),
person(
given = "Martin",
family = "Garrido Rodríguez",
family = "Garrido Rodriguez",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0003-4125-5643")
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7 changes: 7 additions & 0 deletions NEWS.md
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# LIANA 0.1.14 (06.08.24)

- Minor tutorial improvements.

- Remove non-standard symbols from description.


# LIANA 0.1.13 (03.11.23)

- Changed the way that `max` rank is imputed when NAs are presented, or when `return_all` is true.
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14 changes: 14 additions & 0 deletions vignettes/liana_cc2tensor.Rmd
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Expand Up @@ -40,6 +40,20 @@ This tensor is then decomposed into a set of factors, which can be interpreted a
low dimensionality latent variables (vectors) that capture the
CCC patterns across contexts.

## Updated Tutorials


We have written extensive in both Python and R:
https://ccc-protocols.readthedocs.io/en/latest/notebooks/ccc_R/QuickStart.html

We recommend following those, after you setup a conda environment with both LIANA and Tensor-cell2cell following the instructions here:
https://github.com/saezlab/ccc_protocols/tree/main/env_setup

We also recommend using the more efficient and completele version of LIANA - i.e. LIANA+ (in Python):
https://ccc-protocols.readthedocs.io/en/latest/notebooks/ccc_python/QuickStart.html


## Simple (Outdated) Example

Here, we will combine `LIANA` with `tensor_cell2cell` to decipher potential ligand-receptor
interaction changes.
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5 changes: 5 additions & 0 deletions vignettes/liana_tutorial.Rmd
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Expand Up @@ -40,6 +40,11 @@ corresponding resources.

![](ligrec_pipe.png)

## LIANA's development continous as LIANA+

We recommend all users to consider using [LIANA+](https://liana-py.readthedocs.io/en/latest/index.html), instead of LIANA, due to it's increased efficiency and completeness.
We plan to eventually port all LIANA+ functionalities and backend to R, but in the meantime [LIANA+ in Python](https://liana-py.readthedocs.io/en/latest/index.html) is recommended.

## Load required packages
```{r load_pkgs, message=FALSE, warning=FALSE}
library(tidyverse)
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