Ecosyste.ms: Issues

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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

#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

#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

#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

#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

#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

#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

#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

#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

#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

#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