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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level written 1 day ago by meatbelt • 0 • updated 1 day ago by Michael Love ♦ 26k
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Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
edger deseq2 design matrix atac design formula written 2 days ago by corinne_hutfilz • 0 • updated 1 day ago by Michael Love ♦ 26k
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>5000 significantly differentially expressed genes
deseq2 written 1 day ago by liam.childs • 0 • updated 1 day ago by Michael Love ♦ 26k
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Understanding interactions in DESeq2
deseq2 written 2 days ago by benjamin.aaron.taylor • 0 • updated 1 day ago by swbarnes2 • 340
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DESeq2 changing Rownames (Gene accession numbers)
deseq2 written 3 days ago by JGibbons1 • 0
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DESeq2: downregulation of control sample
deseq2 written 3 days ago by raven • 0 • updated 2 days ago by Michael Love ♦ 26k
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Collapse Technical Replicates and Group-specific condition effects, individuals nested within groups
rnaseq deseq2 model.matrix collapsetechnicalreplicates written 3 days ago by rbenel • 0 • updated 3 days ago by Michael Love ♦ 26k
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Help with DESeq2 design matrix
deseq2 written 5 days ago by MGuny • 0 • updated 4 days ago by mona.alee101 • 0
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Does DESeq2 Data_transformation (vsd or rld) Change Clustering (and PCA_plot) Results?
deseq2 rld vsd data transformation ntd written 5 days ago by Arctic • 0 • updated 5 days ago by Michael Love ♦ 26k
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Results counts to Deseq object
deseq2 countmatrix written 6 days ago by Raquel • 0 • updated 5 days ago by Michael Love ♦ 26k
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Comparing factor levels in deseq2
deseq2 written 7 days ago by gv • 40
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Normalized counts access in DESeq2 R: with and without batch
normalization edger deseq2 written 8 days ago by Matan G. • 0 • updated 8 days ago by Michael Love ♦ 26k
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DEseq2 design matrix for paired samples with batch effects
deseq2 written 8 days ago by cylsae • 0 • updated 8 days ago by Michael Love ♦ 26k
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DESeq2 DE analysis of two samples conditioned on a shared reference
deseq2 written 9 days ago by amin.zzia • 0 • updated 8 days ago by Michael Love ♦ 26k
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DESeq2 counts function not working
rnaseq deseq deseq2 written 9 days ago by mrfossl97 • 0 • updated 9 days ago by Michael Love ♦ 26k
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DESeq2: experiment with two genotypes and three conditions
deseq2 written 10 days ago by efratk • 0 • updated 10 days ago by Michael Love ♦ 26k
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how to correct for age using Deseq2
deseq2 written 10 days ago by luca.pagliaroli • 0 • updated 10 days ago by Michael Love ♦ 26k
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How to perform DEseq2 on datasets without replicates or merged replicates
deseq2 R bioconductor replicates rna_seq written 12 days ago by aishu.jp • 20 • updated 10 days ago by swbarnes2 • 340
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DESeq2 using 'relevel' for different comparisons
deseq2 written 11 days ago by Matan G. • 0 • updated 11 days ago by Michael Love ♦ 26k
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Still lots of NA adjusted p-values in DESeq2 after eliminating Cook's distance cutoff.
deseq2 written 11 days ago by ariel • 0
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DESeq2 very complex design - how extract contrasts of interest?
deseq2 rna-seq glm multifactorial design contrasts written 11 days ago by meatbelt • 0 • updated 11 days ago by Michael Love ♦ 26k
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DESeq2: Is it possible to have incomplete pairs of samples?
deseq2 written 12 days ago by microbe • 0 • updated 12 days ago by James W. MacDonald ♦ 52k
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Detecting the power in differential expression
limma edger deseq2 differential expression power written 4 weeks ago by Beginner • 0
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Nested design vs averaging coefficients
deseq2 written 15 days ago by i.sudbery • 10 • updated 15 days ago by Michael Love ♦ 26k
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WGCNA module Eigengene PC1 and expression correlation
deseq2 wgcna rna-seq written 16 days ago by Sri Dewi • 0
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