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passing test_above_log2_fold_change from tidybulk to DESeq2

Status: Open.

#333 In tidyomics/tidybulk;

· stemangiola opened on Oct 14, 2025

Discrepancy in DE results from base DESeq2 and tidybulk DESeq2 method

Status: Open.

#328 In tidyomics/tidybulk;

· MSaadfarooq opened on May 12, 2025

Add example on vignettes and README of how to check for dispersion, and MA plot after DE for egdeR/limma/DESeq2

Status: Open.

#320 In tidyomics/tidybulk;

· stemangiola opened on Dec 18, 2024

The sample data of the <code>test_gene_enrichment()</code> function reports an error and cannot be used.

Status: Open.

#316 In tidyomics/tidybulk;

· zhangkaicr opened on Jul 25, 2024

Add the method to simplify complete confounders is they are not factor of interest

enhancementNew feature or requestNew feature or request

Status: Open.

#301 In tidyomics/tidybulk;

· stemangiola opened on Nov 15, 2023

Prepare for upcoming Seurat v5 release

Status: Open.

#298 In tidyomics/tidybulk;

· Gesmira opened on Oct 3, 2023

the attribute "internals" $ tt_columns abundance_scaled, carries the environment with it inflating the RDS file size

Status: Open.

#295 In tidyomics/tidybulk;

· stemangiola opened on Sep 11, 2023

Improve the documentation for <code>tidybulk</code>

documentationImprovements or additions to documentationImprovements or additions to documentation

good first issueGood for newcomersGood for newcomers

Status: Open.

#282 In tidyomics/tidybulk;

· stemangiola opened on Jul 22, 2023

Warning in CHECK, mistery

Status: Open.

#273 In tidyomics/tidybulk;

· stemangiola opened on Jun 29, 2023

pathway analysis using tidybulk

Status: Open.

#263 In tidyomics/tidybulk;

· adityamahadevaniyer opened on Jan 13, 2023

for SE save internals within the metadata rather than attributes.

enhancementNew feature or requestNew feature or request

Status: Open.

#240 In tidyomics/tidybulk;

· stemangiola opened on Jun 25, 2022

Allow logFC shrinkage in DESeq

enhancementNew feature or requestNew feature or request

Status: Open.

#224 In tidyomics/tidybulk;

· antass opened on Nov 1, 2021