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Issues list

multi-config output organization enhancement New feature or request
#471 opened Jun 10, 2025 by suzannejin
Make "immunedeconv" a "functioanl method" instead of treating it separately enhancement New feature or request
#469 opened Jun 5, 2025 by grst
Meta issue HTML report improvements enhancement New feature or request
#466 opened Jun 2, 2025 by grst
unification of paramsheet and profile enhancement New feature or request
#465 opened May 29, 2025 by suzannejin
6
implement code to parse paramsheet in yaml format enhancement New feature or request
#464 opened May 29, 2025 by suzannejin
Add gene id to VARIANCEPARTITION_DREAM results bug Something isn't working
#463 opened May 27, 2025 by atrigila
@antoniasaracco
Support complex contrasts and models in DESeq2 enhancement New feature or request
#459 opened May 9, 2025 by grst
@atrigila
Support complex contrasts and models in limma enhancement New feature or request
#458 opened May 9, 2025 by grst
@atrigila
v2.0 release plan enhancement New feature or request
#457 opened May 9, 2025 by grst
2
Suggestion: Add PDF Output for Figures (Vector Format) enhancement New feature or request
#456 opened May 8, 2025 by jiehuichen
Allow specification of ANOVA-like contrasts enhancement New feature or request
#455 opened May 6, 2025 by grst
How to generate high-quality PDF files (vector graphics) for GSEA analysis enhancement New feature or request
#453 opened Apr 26, 2025 by jiehuichen
Allow for multiple contrasts to be tested for a single model enhancement New feature or request
#452 opened Apr 17, 2025 by grst
combination of differential analysis methods
#449 opened Apr 7, 2025 by suzannejin
JSON schema: Differentialabundance documentation Improvements or additions to documentation
#445 opened Mar 25, 2025 by jen-reeve
8 of 15 tasks
@kshirlekar
Enable propd inside the pipeline
#433 opened Feb 13, 2025 by suzannejin
3 tasks
minimal test dataset
#432 opened Feb 6, 2025 by suzannejin
2 tasks
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
Add multi-tool logic to workflow
#422 opened Jan 16, 2025 by suzannejin
Error in exploratory plots with --differential_subset_to_contrast_samples bug Something isn't working
#418 opened Jan 6, 2025 by sci-kai
Automatic build of gene set database
#388 opened Dec 11, 2024 by suzannejin
3 tasks
2
Multi-tool functionality and subworkflows as hub of methods
#385 opened Dec 10, 2024 by suzannejin
11 of 25 tasks
16
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
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