liana

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Error in installation

3

I am trying to install liana in R/4.0.2 using remotes::install_github("saezlab/liana") The installation fails with: Error: object ‘homologene_download’ is not exported by 'namespace:OmnipathR' Execution halted I had previous installed OmnipathR using...

rstorch01

Warning: `progress_estimated()` was deprecated in dplyr 1.0.0.

1

Hi ! Running cellphonedb the progrsess bar don't show due to : Warning: `progress_estimated()` was deprecated in dplyr 1.0.0. Thanks !

BenjaminDEMAILLE

Custom Visualizations

3

First, I want to thank you all for making such a useful package and creating informative tutorials to use with other methods for cell-cell communication (NicheNet and Tensor cell2cell). Unless...

RMOsborn012

Omnipath extension

1

Hi liana group, Thank you so much creating this amazing resource. I am trying to extend this to using omnipath to look at specific pathways. I am able to get...

lindsdudley

liana_tensor_c2c error: All input columns must be contained in all dataframes included in 'context_dict'

4

Hi, Thanks for developing LIANA, it's a truly wonderful tool. I'm trying to run tensor decomposition on my data to compare cell-cell communication between two conditions (WT and KO for...

alvarezprado

Development of LIANA keeps going but most of the efforts are currently only in Python - to be ported also to R in the future. Please check: https://liana-py.readthedocs.io/en/latest/ and https://github.com/saezlab/liana-py...

dbdimitrov

Hi Daniel, Thank you for your package, it is very helpful for studying intercellular communication. I tried to add my dataset to liana for analysis before but failed many times....

Tianyi409

How to customise the X-axis order in heat_freq and color in chord_freq

1

Dear Liana team and users, Thanks for great package for being easy to use. After subsetting the data based on the conditions, I want to plot the heatmap with desired...

mainharryHR

Issue with Deprecated Functions and Gene Count Handling in liana_aggregate Function

1

While using the liana_aggregate function in the liana package, I encountered several issues related to deprecated functions and gene filtering. Below is a detailed description of the problems and the...

gomez-dan