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mismatch of documentation and implementation regarding how to specify design for DESeq2.

Status: Open.

#147 In HelenaLC/muscat;

· mschilli87 opened on Oct 30, 2025

There is a large discrepancy between the results obtained from pseudobulk methods and mixed models.

Status: Open.

#145 In HelenaLC/muscat;

· kuangzhuoran opened on Aug 29, 2025

mmDS(method = 'dream')

Status: Open.

#144 In HelenaLC/muscat;

· CHENGHAO-WANG opened on Jun 8, 2025

latent variables

Status: Open.

#138 In HelenaLC/muscat;

· Flu09 opened on Aug 26, 2024

pbDS(pb, design = mm, contrast = contrast) error

Status: Open.

#136 In HelenaLC/muscat;

· Jadeapple opened on Jun 4, 2024

Multiple Random Effects

Status: Open.

#134 In HelenaLC/muscat;

· jgockley62 opened on May 3, 2024

Doubt in sim_mean and ground truth

Status: Open.

#131 In HelenaLC/muscat;

· cakeinspace opened on Dec 28, 2023

limma-voom implementation results in more false positives than expected

Status: Open.

#129 In HelenaLC/muscat;

· reubenthomas opened on Nov 9, 2023

How is the AveExpr in mmDS calculated?

Status: Open.

#127 In HelenaLC/muscat;

· Lila3141 opened on Sep 28, 2023

limma voom cpm values

Status: Open.

#126 In HelenaLC/muscat;

· AnjaliC4 opened on Sep 20, 2023

DP simulated data has inverted logFC and only one bimodal group

Status: Open.

#125 In HelenaLC/muscat;

· ChristophH opened on Aug 14, 2023

pbDS limma-voom method appears to ignore voom weights after computing them

Status: Open.

#119 In HelenaLC/muscat;

· DarwinAwardWinner opened on Mar 21, 2023