Showing: edger • reset
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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 4 days ago by corinne_hutfilz • 0 • updated 11 hours ago by Gordon Smyth ♦ 39k
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EdgeR: Transforming coefficients before testing for differential expression
edger model.matrix contrasts circadian written 5 days ago by ingerslev • 0
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39
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cqn vignette error
normalization edger cqn written 9 days ago by Jenny Drnevich • 1.9k
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92
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Normalized counts access in DESeq2 R: with and without batch
normalization edger deseq2 written 10 days ago by Matan G. • 0 • updated 10 days ago by Michael Love ♦ 26k
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1
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Nested Random Effect in LIMMA: Is It Possible?
limma edger rna-seq random effects written 11 days ago by mjgarcia • 0 • updated 11 days ago by Gordon Smyth ♦ 39k
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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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70
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Difference between Fold Changes from EdgeR glmLRTest and directly calculated fold changes.
edger rna seq written 20 days ago by abf • 0 • updated 19 days ago by James W. MacDonald ♦ 52k
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1
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62
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"filterByExpr" Function filtered out all my counts
edger written 21 days ago by qicaibiology • 10 • updated 21 days ago by Gordon Smyth ♦ 39k
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88
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edgeR lable shuffling permutation test
edger written 24 days ago by d.ricken • 0 • updated 24 days ago by Gordon Smyth ♦ 39k
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476
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EdgeR RNAseq -- best way to deal with random effects
rnaseq edger written 13 months ago by emb13 • 0 • updated 25 days ago by gil.hornung • 0
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2
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103
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adding "symbol" column in my differential expressed genes in EdgeR
edger written 28 days ago by alihakimzadeh73 • 0 • updated 27 days ago by James W. MacDonald ♦ 52k
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3
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107
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interpreting FC values from glmTreat, especially unshrunk log-fold-changes
edger glmtreat significance testing written 4 weeks ago by flemi221 • 0 • updated 4 weeks ago by Yunshun Chen • 540
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103
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removing genes before RNA-seq normalization
normalization edger deseq2 removing genes written 4 weeks ago by aec • 50 • updated 4 weeks ago by Gordon Smyth ♦ 39k
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Filtering lowly-expressed genes in a RNASeq dataset with continuous instead of grouping variables
limma edger written 5 weeks ago by anniina.mattila • 0 • updated 5 weeks ago by James W. MacDonald ♦ 52k
3
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92
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Nested Interaction in edgeR and composition bias
edger rna-seq written 6 weeks ago by chapdelainev • 0 • updated 6 weeks ago by Gordon Smyth ♦ 39k
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1
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edgeR or DESeq2 between duplicated chromosomes in the same individual
normalization edger deseq2 dge written 7 weeks ago by grant.dejong • 0 • updated 6 weeks ago by Gordon Smyth ♦ 39k
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97
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Account for inter individual variability at the baseline using nested models
limma edger written 6 weeks ago by Zeel • 0 • updated 6 weeks ago by Gordon Smyth ♦ 39k
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3
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EdgeR DGElist - equal counts between treatment and control incorrectly give significant PValue using estimateGLMCommonDisp through DGElist
edger written 7 weeks ago by khyu • 10 • updated 7 weeks ago by Gordon Smyth ♦ 39k
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1
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96
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Very variable samples vs similar samples in the same dataset
edger deseq2 written 7 weeks ago by eduardogccm • 0 • updated 7 weeks ago by Michael Love ♦ 26k
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85
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log2FC calculation in EdgeR
edger log2fc written 7 weeks ago by matteo.buti • 0 • updated 7 weeks ago by James W. MacDonald ♦ 52k
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"adding gene annotations" in edgeR doesn't work with select()
edger deg written 8 weeks ago by mjavad2012 • 0 • updated 8 weeks ago by James W. MacDonald ♦ 52k
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edgeR time series analysis with no replicates
edger written 4.2 years ago by sirintra • 10 • updated 8 weeks ago by owuorerick • 0
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Multiple samples per individual and unbalanced number of samples per individual: DE between groups still an ordinary two-group comparison?
limma edger deseq2 differential expression repeated measures written 10 weeks ago by hermidalc • 0
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DESeq2 VS edgeR DEG results different in analysis same data
edger deseq2 written 10 weeks ago by 15958021290 • 0 • updated 10 weeks ago by Gordon Smyth ♦ 39k
7
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Bug in estimateDisp of "edgeR"? "weights' matched by multiple actual arguments
edger estimatedisp written 10 weeks ago by Sandip Darji • 10 • updated 10 weeks ago by Gordon Smyth ♦ 39k
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