Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / saezlab/decoupler-py issues and pull requests
#147 - Failure with .get_pseudobulk() when grouping/sample columns are categorical
Issue -
State: open - Opened by dnjst about 2 months ago
Labels: bug
#146 - dc.get_pseudobulk needs to use '.todense()' instead of '.A'
Issue -
State: closed - Opened by jhaberbe 2 months ago
- 2 comments
Labels: bug
#145 - implement z-score method
Pull Request -
State: closed - Opened by smuellerd 2 months ago
#144 - Marsilea error in dc.plot_associations()
Issue -
State: open - Opened by dnjst 3 months ago
- 1 comment
Labels: bug
#143 - Update pre
Pull Request -
State: closed - Opened by Intron7 3 months ago
#142 - Dataloading
Issue -
State: closed - Opened by Intron7 3 months ago
- 1 comment
Labels: question
#141 - Error when running get_pseudobulk(): AttributeError: 'csr_matrix' object has no attribute 'A'
Issue -
State: open - Opened by raquelgarza 3 months ago
- 2 comments
Labels: bug
#140 - Warnings about annotations raised when running `dc.plot_targets`
Issue -
State: closed - Opened by Fantasque68 3 months ago
- 1 comment
Labels: bug
#139 - AttributeError: 'csr_matrix' object has no attribute 'A'
Issue -
State: closed - Opened by MarwaneBourdim 3 months ago
- 6 comments
Labels: bug
#138 - psbulk_counts are associated with top PCs
Issue -
State: closed - Opened by singlecellfan 3 months ago
- 5 comments
Labels: question
#137 - module 'decoupler' has no attribute 'plot_network'
Issue -
State: closed - Opened by linanzhang 3 months ago
- 1 comment
Labels: question
#136 - updates f-array
Pull Request -
State: closed - Opened by Intron7 3 months ago
#135 - numba version 0.60.0
Issue -
State: closed - Opened by Intron7 3 months ago
- 6 comments
Labels: bug
#134 - Transition to `poetry` + address `numpy 2.0` and `numba 0.60` related issues
Pull Request -
State: closed - Opened by deeenes 3 months ago
- 4 comments
#133 - Inferring TF activity using custom GRN
Issue -
State: closed - Opened by AmelZulji 4 months ago
- 4 comments
Labels: question
#132 - GSEA handling missing genes
Issue -
State: closed - Opened by tboen1 4 months ago
- 5 comments
Labels: question
#131 - Issue with omnipath and dc.translate_net(msigdb, target_organism = 'mouse', unique_by = ('geneset', 'genesymbol'))
Issue -
State: closed - Opened by dantyrr 4 months ago
- 3 comments
Labels: bug
#130 - Detection of type of alteration in each signaling pathway in each cell type
Issue -
State: closed - Opened by ngvananh2508 4 months ago
- 6 comments
Labels: question
#129 - keyerror when running dc.get_ora_df
Issue -
State: closed - Opened by wangjiawen2013 4 months ago
- 1 comment
Labels: bug
#128 - Progeny mouse 'Invalid block type' error
Issue -
State: closed - Opened by eaboelno 4 months ago
- 4 comments
Labels: question, database/omnipath
#127 - matplotlib.cm.get_cmap is removed from version 3.9
Issue -
State: closed - Opened by zhaleh-safikhani 4 months ago
- 2 comments
Labels: bug
#126 - ORA analysis get hung in jupyter notebook
Issue -
State: closed - Opened by zhaleh-safikhani 4 months ago
- 1 comment
Labels: question
#125 - plot_network doesnt return a graph with right node/edge visual styles
Issue -
State: closed - Opened by zhaleh-safikhani 5 months ago
- 1 comment
Labels: bug
#124 - Getting pval=0 for various enriched pathways after running GSEA
Issue -
State: closed - Opened by saksham132 5 months ago
- 2 comments
Labels: question
#123 - Problem when using dc.get_contrast()
Issue -
State: closed - Opened by derekchen7 5 months ago
- 2 comments
Labels: question
#122 - Progeny pvals
Issue -
State: closed - Opened by nicolebussola 5 months ago
- 1 comment
Labels: question
#121 - Gene Symbols from Ensembl or custom source + better handling of identifiers and orthology translation
Pull Request -
State: closed - Opened by deeenes 5 months ago
- 1 comment
#120 - why ulm (and not mlm) for transription factor activities ? there must be some overlaps
Issue -
State: closed - Opened by Sophon-0 5 months ago
- 1 comment
Labels: question
#119 - plot_network function top target
Issue -
State: closed - Opened by Sophon-0 5 months ago
- 1 comment
Labels: question
#118 - Is run_aucell thread-safe to run in a multi-threaded script?
Issue -
State: closed - Opened by pcm32 6 months ago
- 3 comments
Labels: question
#117 - run_ulm on TF with only positively regulated target genes
Issue -
State: closed - Opened by ken-chen-18 6 months ago
- 2 comments
Labels: question
#115 - dc.run_mlm only returning data for 1 source
Issue -
State: closed - Opened by aalockhart1 6 months ago
- 2 comments
Labels: question
#114 - PLOT issues
Issue -
State: closed - Opened by Sophon-0 6 months ago
- 2 comments
Labels: question
#113 - Update Dockerfile
Pull Request -
State: closed - Opened by Nic-Nic 6 months ago
Labels: version
#112 - Docker building via github action
Pull Request -
State: closed - Opened by gabora 6 months ago
#111 - Verbose output from bencharking pipeline seems to say 'for 25 unique sources' despite more sources
Issue -
State: closed - Opened by IBMB-MFP 7 months ago
- 2 comments
Labels: bug
#110 - Cannot convert gene symbol to rat
Issue -
State: closed - Opened by wangjiawen2013 7 months ago
- 5 comments
Labels: bug, database/omnipath
#109 - Error while translating human to mouse MSigDB
Issue -
State: closed - Opened by wbrett87 7 months ago
- 6 comments
Labels: database/omnipath, networking
#108 - Failed to download `CollecTRI` from OmniPath. Invalid value `loops` for `InteractionsQuery`. AttributeError: module 'omnipath' has no attribute 'static'
Issue -
State: closed - Opened by clg12 7 months ago
- 1 comment
Labels: database/omnipath
#107 - copy.deepcopy() in get_contrast()
Issue -
State: closed - Opened by wan-nie 7 months ago
- 2 comments
Labels: bug
#106 - Nan values in benchmarking pipeline still give error - Decoupler v 1.6
Issue -
State: closed - Opened by IBMB-MFP 7 months ago
- 2 comments
Labels: documentation
#105 - EOFError: Compressed file ended before the end-of-stream marker was reached
Issue -
State: closed - Opened by ChangLu92 7 months ago
- 2 comments
Labels: database/omnipath, networking
#104 - decoupler.plot_barplot ax
Issue -
State: closed - Opened by annita-louloupi 7 months ago
- 3 comments
Labels: question
#103 - Flag for sorting of gene names
Issue -
State: closed - Opened by leoTiez 8 months ago
- 4 comments
Labels: question
#102 - Loading resources for mouse is not working
Issue -
State: closed - Opened by riederd 8 months ago
- 9 comments
Labels: bug
#101 - run_ora_df
Issue -
State: closed - Opened by mcjmigdal 8 months ago
- 2 comments
Labels: question
#100 - Fix formatting
Pull Request -
State: closed - Opened by Zethson 9 months ago
- 1 comment
#99 - Limiting usage of cores or threads
Issue -
State: closed - Opened by racng 9 months ago
- 2 comments
Labels: question
#97 - Announcement: some Galaxy modules for some decoupler functionalities
Issue -
State: closed - Opened by pcm32 10 months ago
- 1 comment
Labels: question
#96 - Tutorial clustermap changed to Marsilea
Pull Request -
State: closed - Opened by shuang1330 10 months ago
- 2 comments
#95 - dc.get_collectri() does not work
Issue -
State: closed - Opened by FADHLyemen 10 months ago
- 2 comments
Labels: question, database/omnipath
#94 - Functional PB Tutorial fails at dc.plot_associations
Issue -
State: closed - Opened by jan-engelmann 10 months ago
- 5 comments
Labels: bug
#93 - ValueError: Invalid value `loops` for `InteractionsQuery` in dc.get_collectri()
Issue -
State: closed - Opened by GERMAN00VP 10 months ago
- 2 comments
#92 - dc.get_progeny(organism = 'mouse') fails with ImportError
Issue -
State: closed - Opened by riederd 10 months ago
- 5 comments
Labels: bug
#91 - Get gene markers used to annotate the cell type
Issue -
State: closed - Opened by ryrl9703 10 months ago
- 2 comments
Labels: question
#90 - Method dc.run_gsva error
Issue -
State: closed - Opened by chuiqin 11 months ago
- 2 comments
Labels: bug
#89 - Pseudobulk for each sample
Issue -
State: closed - Opened by SNOL2 11 months ago
- 2 comments
Labels: question
#88 - method run_gsea() error : SystemError: CPUDispatcher(<function nb_gsea at 0x7f7477d3b9c0>) returned a result with an exception set
Issue -
State: closed - Opened by nicolas-zimmermann 11 months ago
- 6 comments
Labels: bug
#87 - shuffle_net output not random
Issue -
State: closed - Opened by IBMB-MFP 11 months ago
- 1 comment
Labels: bug
#86 - Error downlaoding progeny model for mouse species
Issue -
State: closed - Opened by archanabhardwaj 11 months ago
- 3 comments
Labels: question
#85 - Problems running decoupleR with Compressed Sparse Column (csc) count matrix
Issue -
State: closed - Opened by vckraemer 11 months ago
- 2 comments
Labels: bug
#84 - Switching to conda forge
Issue -
State: closed - Opened by wxicu 12 months ago
- 7 comments
Labels: question
#83 - use of the run_gsva method : format of the net argument
Issue -
State: closed - Opened by nicolas-zimmermann 12 months ago
- 1 comment
Labels: question
#82 - Module request: UCell signatures
Issue -
State: closed - Opened by pcm32 12 months ago
- 2 comments
Labels: question
#81 - shuffle_nets function produces networks with repeated edges
Issue -
State: closed - Opened by IBMB-MFP 12 months ago
- 1 comment
Labels: bug
#80 - Differential expression error in pseudo-bulk step
Issue -
State: closed - Opened by dfermin about 1 year ago
- 4 comments
Labels: bug
#79 - removes dtype from anndata
Pull Request -
State: closed - Opened by Intron7 about 1 year ago
- 1 comment
#78 - get_metadata_associations - TypeError: data type 'category' not understood
Issue -
State: closed - Opened by ttszen about 1 year ago
- 7 comments
Labels: question
#77 - Using decoupler to implement Cytosig analysis
Issue -
State: closed - Opened by SNOL2 about 1 year ago
- 2 comments
Labels: question
#76 - How does run_aucell receive the gene signatures?
Issue -
State: closed - Opened by pcm32 about 1 year ago
- 1 comment
Labels: question
#75 - A recommendation for prior network preprocessing based on expression data
Issue -
State: closed - Opened by janursa about 1 year ago
- 7 comments
#74 - Changed minimal possible value for min_counts to zero
Pull Request -
State: closed - Opened by Claptar about 1 year ago
#73 - Clipping of `min_counts` in `get_pseudobulk`
Issue -
State: closed - Opened by Claptar about 1 year ago
- 4 comments
#72 - Error when using get_collectri, but not get_dorothea
Issue -
State: closed - Opened by ken-chen-18 about 1 year ago
- 6 comments
Labels: question
#71 - dc.get_collectri and dc.get_dorothea fails with errors in the Google Colab
Issue -
State: closed - Opened by hengkp about 1 year ago
- 6 comments
Labels: database/omnipath
#70 - Adds seaborn to dependencies
Pull Request -
State: closed - Opened by pcm32 about 1 year ago
- 1 comment
#69 - Shouldn't decoupler require seaborn as a dependency?
Issue -
State: closed - Opened by pcm32 about 1 year ago
- 2 comments
Labels: question
#68 - Input for bulk analysis when dealing with batch effet
Issue -
State: closed - Opened by merlevede about 1 year ago
- 5 comments
Labels: question
#67 - run_aucell extracts the features from adata.var.index implicitly without any option to change this
Issue -
State: closed - Opened by radutanasa about 1 year ago
- 2 comments
#66 - Include unique identifiers for GO terms?
Issue -
State: closed - Opened by brainfo about 1 year ago
- 4 comments
Labels: question
#65 - dc.run_mlm() and dc.get_gsea_df()
Issue -
State: closed - Opened by dyinboisry4u about 1 year ago
- 1 comment
Labels: question
#64 - ValueError: Invalid value `loops` for `InteractionsQuery`.
Issue -
State: closed - Opened by janursa about 1 year ago
- 4 comments
Labels: bug
#63 - Editing plots using matplotlib
Issue -
State: closed - Opened by alpha-1-centauri about 1 year ago
- 2 comments
Labels: question
#62 - Updated benchmark to remove NAs in activities
Pull Request -
State: closed - Opened by smuellerd about 1 year ago
#61 - Check other options besides csr_matrix in check_X inside get_pseudobulk
Issue -
State: closed - Opened by roramirezf about 1 year ago
- 4 comments
Labels: bug
#60 - updated docs
Pull Request -
State: closed - Opened by demian1 about 1 year ago
#59 - Regarding the function 'get_metadata_association'
Issue -
State: closed - Opened by Phil-Momoka about 1 year ago
- 4 comments
Labels: question
#58 - association between embeddings and sample metadata using simple anova model
Pull Request -
State: closed - Opened by demian1 about 1 year ago
#57 - Pseudobulk looses some samples
Issue -
State: closed - Opened by grst about 1 year ago
- 2 comments
Labels: bug
#56 - run_ora using adata as the input
Issue -
State: closed - Opened by biopzhang about 1 year ago
- 3 comments
Labels: bug, enhancement
#55 - Error importing decoupler library in python
Issue -
State: closed - Opened by aimorenov-owkin about 1 year ago
- 4 comments
#54 - dc.get_resource("MSigDB", organism = "mouse") fails with errors in pypath
Issue -
State: closed - Opened by Christian-Heyer over 1 year ago
- 4 comments
Labels: bug
#52 - enr_pvals Ora method
Issue -
State: closed - Opened by ACheccoli over 1 year ago
- 2 comments
Labels: bug
#51 - ChunkedEncodingError in downloading msigDB
Issue -
State: closed - Opened by ACheccoli over 1 year ago
- 7 comments
Labels: database/omnipath
#50 - Weird reindexing
Issue -
State: closed - Opened by ACheccoli over 1 year ago
- 6 comments
Labels: bug
#49 - rank_sources_groups
Issue -
State: closed - Opened by cdiaz45 over 1 year ago
- 3 comments
Labels: bug
#48 - Would you have any recommendation for running Pathway activity inference when we don't have any controls?
Issue -
State: closed - Opened by jasiozaucha over 1 year ago
- 1 comment
Labels: question
#47 - How do you use the run_gsea method with an expression data frame (like a DESeq2 result)?
Issue -
State: closed - Opened by pcm32 over 1 year ago
- 1 comment
Labels: question
#44 - Are dc.run_consensus p-values valid?
Issue -
State: closed - Opened by pcm32 over 1 year ago
- 2 comments
Labels: question
#43 - run_ora
Issue -
State: closed - Opened by elektrafying2000 over 1 year ago
- 1 comment
Labels: question