The Bionconductor Core Team, Alejandro Reyes, Andrzej Oles, Aleksandra Pekowska, Felix Klein, Nikolaos Ignatiadis (IHW), Anqi Zhu (apeglm), Joseph Ibrahim (apeglm), Vince Carey, Owen Solberg, Ruping Sun, Devon Ryan, Steve Lianoglou, Jessica Larson, Christina Chaivorapol, Pan Du, Richard Bourgon, Willem Talloen, Elin Videvall, Hanneke van Deutekom, Todd Burwell, Jesse Rowley, Igor Dolgalev, Stephen Turner, Ryan C Thompson, Tyr Wiesner-Hanks, Konrad Rudolph, David Robinson, Mingxiang Teng, Mathias Lesche, Sonali Arora, Jordan Ramilowski, Ian Dworkin, Bjorn Gruning, Ryan McMinds, Paul Gordon, Leonardo Collado Torres, Enrico Ferrero, Peter Langfelder, Gavin Kelly, Rob Patro, Charlotte Soneson, Koen Van den Berge, Fanny Perraudeau, Davide Risso, Stephan Engelbrecht, Nicolas Alcala, Jeremy Simon, Travis Ptacek, Rory Kirchner, R. We have benefited in the development of DESeq2 from the help and feedback of many individuals, including but not limited to: I have trouble installing DESeq2 on Ubuntu/Linux…Ĭonstantin Ahlmann-Eltze has contributed core code for increasing the computational performance of DESeq2 and building an interface to his glmGamPoi package.I want to benchmark DESeq2 comparing to other DE tools.Is there an official Galaxy tool for DESeq2?.What are the exact steps performed by DESeq()?.I ran a likelihood ratio test, but results() only gives me one comparison.How can I include a continuous covariate in the design formula?.Can I use DESeq2 to analyze a dataset without replicates?.Can I run DESeq2 to contrast the levels of many groups?.If I have multiple groups, should I run all together or split into pairs of groups?.Can I use DESeq2 to analyze paired samples?.Do normalized counts correct for variables in the design?.Why after VST are there still batches in the PCA plot?.How do I use VST or rlog data for differential testing?.How can I get unfiltered DESeq2 results?.Independent filtering and multiple testing.Methods changes since the 2014 DESeq2 paper.Group-specific condition effects, individuals nested within groups.Sample-/gene-dependent normalization factors.Tests of log2 fold change above or below a threshold.Dispersion plot and fitting alternatives.Recommendations for single-cell analysis.Extended section on shrinkage estimators.Control features for estimating size factors.Principal component plot of the samples.Heatmap of the sample-to-sample distances.
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