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66 Open 127 Closed
66 Open 127 Closed
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Issues list

Enable propd inside the pipeline
#433 opened Feb 13, 2025 by suzannejin
3 tasks
@suzannejin
minimal test dataset
#432 opened Feb 6, 2025 by suzannejin
2 tasks
Switch to formula-based model definition enhancement New feature or request
#429 opened Jan 30, 2025 by grst
@nschcolnicov
Centralized option to set seed for all non-deterministic methods enhancement New feature or request
#425 opened Jan 22, 2025 by grst
Handle Rmarkdown reports for new methods
#424 opened Jan 22, 2025 by suzannejin
Use toolsheet channel to handle the calls to methods
#423 opened Jan 22, 2025 by suzannejin
Add multi-tool logic to workflow
#422 opened Jan 16, 2025 by suzannejin
3 tasks
Error in exploratory plots with --differential_subset_to_contrast_samples bug Something isn't working
#418 opened Jan 6, 2025 by sci-kai
Merge dev_tmp branch and revert CI changes
#411 opened Dec 20, 2024 by nschcolnicov
@atrigila @nschcolnicov
2
deseq modules displaying full meta as tag instead of meta.id
#403 opened Dec 12, 2024 by nschcolnicov
Automatic build of gene set database
#388 opened Dec 11, 2024 by suzannejin
3 tasks
2
How to define complex contrasts? enhancement New feature or request
#386 opened Dec 10, 2024 by grst
1
Multi-tool functionality and subworkflows as hub of methods
#385 opened Dec 10, 2024 by suzannejin
10 of 22 tasks
14
Contrast specification enhancement New feature or request
#377 opened Dec 6, 2024 by grst
Model validation enhancement New feature or request
#371 opened Dec 3, 2024 by grst
6 tasks done
@atrigila @alanmmobbs93
4
Consider splitting quarto reports into QC and results enhancement New feature or request
#369 opened Dec 3, 2024 by grst
Meta issue functional analyses enhancement New feature or request
#367 opened Dec 3, 2024 by grst
3
Shinylive for ShinyNGS app enhancement New feature or request
#366 opened Dec 3, 2024 by grst
Support SummarizedExperiment as input enhancement New feature or request
#365 opened Dec 3, 2024 by grst
9
Incorrect tab names in differential report bug Something isn't working
#364 opened Dec 3, 2024 by grst
@atrigila @alanmmobbs93 @nschcolnicov
Support for linear mixed effects models via DREAM enhancement New feature or request
#363 opened Dec 2, 2024 by grst
2
More flexible model and contrast definition enhancement New feature or request
#362 opened Dec 2, 2024 by grst
@nschcolnicov
11
Create subworkflow for deconvolution analyses in bulk data enhancement New feature or request
#361 opened Nov 19, 2024 by apeltzer
1 task done
Unable to run pipeline – please provide test data bug Something isn't working
#358 opened Nov 15, 2024 by febedtu
1
Replace unmaintained Proteus with maxLFQ, by author's suggestion. enhancement New feature or request
#356 opened Nov 15, 2024 by vmkalbskopf
ProTip! What’s not been updated in a month: updated:<2025-01-25.