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2
votes
1
answer
46
views
1
answer
"adding gene annotations" in edgeR doesn't work with select()
edger deg written 3 days ago by mjavad2012 • 0 • updated 3 days ago by James W. MacDonald ♦ 51k
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5
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1.9k
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5
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edgeR time series analysis with no replicates
edger written 4.1 years ago by sirintra • 10 • updated 4 days ago by owuorerick • 0
3
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1
answer
154
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1
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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 13 days ago by hermidalc • 0
3
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1
answer
75
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1
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DESeq2 VS edgeR DEG results different in analysis same data
edger deseq2 written 12 days ago by 15958021290 • 0 • updated 12 days ago by Gordon Smyth ♦ 38k
7
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2
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83
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2
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Bug in estimateDisp of "edgeR"? "weights' matched by multiple actual arguments
edger estimatedisp written 14 days ago by Sandip Darji • 10 • updated 13 days ago by Gordon Smyth ♦ 38k
7
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2
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75
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2
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Does edgeR need to specify reference group?
edger reference group written 16 days ago by 15958021290 • 0 • updated 15 days ago by Gordon Smyth ♦ 38k
0
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1
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39
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1
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Variation in the estimation of the common dispersion
edger common dispersion written 17 days ago by hz_67 • 0 • updated 16 days ago by Gordon Smyth ♦ 38k
5
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2
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151
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2
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RNASeq DE analysis starts from different DESeq2 normalized data, TMM normalized data and CPM
limma edger written 18 days ago by li.zhaoz • 0 • updated 17 days ago by Gordon Smyth ♦ 38k
3
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1
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75
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1
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How to normalize RNA-seq data if majority of transcripts expected to be differentially expressed vs control condition?
rnaseq edger written 18 days ago by gdeniz • 0 • updated 18 days ago by Gordon Smyth ♦ 38k
2
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1
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56
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1
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Order of design matrix for edgeR analysis
edger R written 19 days ago by lornaas • 0 • updated 19 days ago by James W. MacDonald ♦ 51k
2
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1
answer
93
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1
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Applying norm.factors in RNA-seq analysis to other expression data by using edgeR
edger written 26 days ago by 2002ymx02 • 0 • updated 26 days ago by Gordon Smyth ♦ 38k
6
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1
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127
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1
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EdgeR - Complex design - contrasts/coefficients
edger glm written 4 weeks ago by D • 0 • updated 4 weeks ago by Yunshun Chen • 490
1
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1
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91
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1
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cpm filtering parameter
rnaseq edger transcriptomics cpm filtering metatranscriptomics written 5 weeks ago by vm.higareda • 0 • updated 5 weeks ago by Gordon Smyth ♦ 38k
5
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2
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111
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2
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is our edgeR code doing what we think it does?
edger differential expression rna-seq written 6 weeks ago by acs1990 • 10 • updated 6 weeks ago by Yunshun Chen • 490
0
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1
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110
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1
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Different Expression Analysis with EDASeq,DESeq2,edgeR,RUVSeq
normalization edger deseq2 ruvg written 7 weeks ago by Yang WY • 0 • updated 7 weeks ago by Michael Love ♦ 25k
2
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1
answer
116
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1
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Design for introducing batch effect in DESeq2
edger deseq2 combat rna-seq batch effect written 7 weeks ago by ag1805x • 20 • updated 7 weeks ago by swbarnes2 • 330
0
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0
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117
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0
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How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
limma biomart edger rna-seq egsea written 7 weeks ago by fgol • 10
0
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1
answer
52
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1
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Searching for responsive genes along with a continuous variable, in environmental experimental design
edger written 7 weeks ago by avihai.zolti • 0 • updated 7 weeks ago by Gordon Smyth ♦ 38k
2
votes
1
answer
87
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1
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edgeR default normalization method
edger written 7 weeks ago by Homer • 0 • updated 7 weeks ago by Gordon Smyth ♦ 38k
1
vote
1
answer
118
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1
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Use intercept or not in model matrix for edgeR methylation analysis
edger methylation R glm written 7 weeks ago by sabrina.mcnew • 0
1
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0
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94
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0
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Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edger salmon written 8 weeks ago by konstantinos.bogias • 10
0
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1
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73
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1
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The meaning of interaction terms in design matrix in edgeR User's Guide on page 38
edger written 9 weeks ago by 2002ymx02 • 0 • updated 9 weeks ago by Gordon Smyth ♦ 38k
0
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1
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96
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1
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Sai Nikhith Cholleti
edger deseq2 written 9 weeks ago by sainikhith508001 • 0 • updated 9 weeks ago by Michael Love ♦ 25k
0
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1
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229
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1
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analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma edger deseq2 combat scrnaseq written 11 weeks ago by Bogdan • 580 • updated 9 weeks ago by Andrew_McDavid • 190
1
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1
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96
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Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
edger written 9 weeks ago by 2002ymx02 • 0 • updated 9 weeks ago by Gordon Smyth ♦ 38k
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