saezlab / decoupler-py

Python package to perform enrichment analysis from omics data.

https://decoupler-py.readthedocs.io/

saezlab/decoupler-py Issues

Is run_aucell thread-safe to run in a multi-threaded script?
Closed a month ago3
run_ulm on TF with only positively regulated target genes
Closed a month ago2
Error while translating human to mouse MSigDB
Closed a month ago6
Failed to download `CollecTRI` from OmniPath. Invalid value `loops` for `InteractionsQuery`. AttributeError: module 'omnipath' has no attribute 'static'
Closed a month ago1
PLOT issues
Closed 2 months ago2
dc.run_mlm only returning data for 1 source
Closed 2 months ago2
Loading resources for mouse is not working
Closed 2 months ago9
EOFError: Compressed file ended before the end-of-stream marker was reached
Closed 2 months ago2
Verbose output from bencharking pipeline seems to say 'for 25 unique sources' despite more sources
Closed 2 months ago2
Cannot convert gene symbol to rat
Closed 2 months ago5
Nan values in benchmarking pipeline still give error - Decoupler v 1.6
Closed 3 months ago2
decoupler.plot_barplot ax
Closed 3 months ago3
copy.deepcopy() in get_contrast()
Closed 3 months ago2
Switching to conda forge
Closed 3 months ago7
Flag for sorting of gene names
Closed 3 months ago4
run_ora_df
Closed 4 months ago2
Limiting usage of cores or threads
Closed 5 months ago2
Functional PB Tutorial fails at dc.plot_associations
Closed 5 months ago5
Get gene markers used to annotate the cell type
Closed 5 months ago2
Announcement: some Galaxy modules for some decoupler functionalities
Closed 5 months ago1
Method dc.run_gsva error
Closed 6 months ago2
method run_gsea() error : SystemError: CPUDispatcher(<function nb_gsea at 0x7f7477d3b9c0>) returned a result with an exception set
Closed 6 months ago6
dc.get_collectri() does not work
Closed 6 months ago2
dc.get_progeny(organism = 'mouse') fails with ImportError
Closed 6 months ago5
ValueError: Invalid value `loops` for `InteractionsQuery` in dc.get_collectri()
Closed 6 months ago2
shuffle_net output not random
Closed 6 months ago1
Error downlaoding progeny model for mouse species
Closed 6 months ago3
Clipping of `min_counts` in `get_pseudobulk`
Closed 7 months ago4
Pseudobulk for each sample
Closed 7 months ago2
get_metadata_associations - TypeError: data type 'category' not understood
Closed 7 months ago7
Problems running decoupleR with Compressed Sparse Column (csc) count matrix
Closed 7 months ago2
use of the run_gsva method : format of the net argument
Closed 7 months ago1
shuffle_nets function produces networks with repeated edges
Closed 7 months ago1
Differential expression error in pseudo-bulk step
Closed 7 months ago4
Module request: UCell signatures
Closed 8 months ago2
How does run_aucell receive the gene signatures?
Closed 8 months ago1
Using decoupler to implement Cytosig analysis
Closed 8 months ago2
Error when using get_collectri, but not get_dorothea
Closed 8 months ago6
A recommendation for prior network preprocessing based on expression data
Closed 8 months ago7
Include unique identifiers for GO terms?
Closed 9 months ago4
Input for bulk analysis when dealing with batch effet
Closed 9 months ago5
Shouldn't decoupler require seaborn as a dependency?
Closed 9 months ago2
dc.get_collectri and dc.get_dorothea fails with errors in the Google Colab
Closed 9 months ago6
dc.run_mlm() and dc.get_gsea_df()
Closed 9 months ago1
ValueError: Invalid value `loops` for `InteractionsQuery`.
Closed 9 months ago4
run_aucell extracts the features from adata.var.index implicitly without any option to change this
Closed 9 months ago2
Editing plots using matplotlib
Closed 9 months ago2
Check other options besides csr_matrix in check_X inside get_pseudobulk
Closed 10 months ago4
Regarding the function 'get_metadata_association'
Closed 10 months ago4
Pseudobulk looses some samples
Closed 10 months ago2