Daniel Dimitrov

external_filters.h:1:9: error: no macro name given in #define directive

9

Hi @grimbough, I'm trying to install rhdf5 (SingleCellExperiment really), but I encounter the following error when trying to install from BioConductor: [removed image as it contains personal paths] and another...

Homology conversion

1

Hi @deeenes, I have implemented the homology conversion that I use in LIANA in OmnipathR. You will notice that it deals with one-to-many as well as with protein complexes. The...

Extend the Chord diagram /w communication strength on e.g. `LRscore` following filtering by `aggregate_rank`.

Unexpected behaviour

1

Hi, Thanks for making such a easy-to-use and well documented package! I was using it and noticed that my adata object got modified and essentially broke my pipeline downstream. Please,...

Related to https://github.com/biocypher/metalinks/issues/4

CellPhoneDB v5 (update and is_ppi flag)

13

Hey Denes, Recently, CellPhoneDB got bumped to v5, and the data is stored here: https://github.com/ventolab/cellphonedb-data/tree/master Seems to have changed format from: https://github.com/saezlab/pypath/blob/bf81f34120b82157fa3ebc15d39b0489b97fbe5e/pypath/resources/urls.py#L1103 Let me know if I can help with...

Hey @deeenes , Recently, MultiNichenet came out, along with it's own LR prior knowledge. Seems to take OmniPath and filter certain interactions that don't necessarily make sense. Available via: `lr_network

Oma

1

Response to #137

Passing filter parameters to pbDS

1

Hi @CATALYST-project, Thanks for maintaining this super useful package. I made a small change to the `pbDS` function so that the parameters used by `edgeR::filterByExpr` and `nmads` are modifiable by...

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...