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0
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0
answers
10
views
0
answers
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma edger deseq deseq2 written 18 minutes ago by Nik Tuzov • 50
10
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1
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5 follow
1
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Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq limma edger deseq2 voom written 2.3 years ago by Sean Davis ♦ 20k • updated 2 days ago by Paul Harrison • 60
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1
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40
views
1
answer
differentially expressed genes form RSEM genes data
rnaseq edger written 3 days ago by lily • 10 • updated 3 days ago by Gordon Smyth ♦ 31k
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0
answers
59
views
0
answers
topGO - missing value where TRUE/FALSE needed
topgo edger written 6 days ago by mictadlo • 0
3
votes
1
answer
46
views
1
answer
Saving output from glmTreat to a csv file?
edger rna-seq written 6 days ago by mictadlo • 0 • updated 6 days ago by Aaron Lun • 16k
1
vote
1
answer
64
views
1
answer
Does edgeR accept decimal / integer read counts for differential expression ?
edger differential gene expression written 7 days ago by Padhmanand.Sudhakar • 0 • updated 6 days ago by Gordon Smyth ♦ 31k
8
votes
1
answer
103
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1
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Why edgeR::aveLogCPM() is simlar to log2(rowMeans(cpm)) instead of rowMeans(cpm(y, log=TRUE))
rnaseq limma edger independent filtering written 10 days ago by Robert Castelo • 2.0k
0
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1
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109
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1
answer
bias.data vector must have the same length as DEgenes vector!
edger goseq written 10 days ago by mictadlo • 0 • updated 10 days ago by Aaron Lun • 16k
3
votes
1
answer
97
views
1
answer
adding genes to edgeR
edger written 10 days ago by mictadlo • 0 • updated 10 days ago by Aaron Lun • 16k
0
votes
1
answer
134
views
1
answer
goseq after edgeR
edger goseq written 14 days ago by mictadlo • 0 • updated 14 days ago by Aaron Lun • 16k
0
votes
0
answers
176
views
0
answers
how to build gene.pathway data.frame for non-model organism
limma topgo edger kegg dataframe written 18 days ago by mictadlo • 0
2
votes
1
answer
75
views
1
answer
differentially expressed miRNA using edge R
edger written 19 days ago by lily • 10 • updated 18 days ago by Gordon Smyth ♦ 31k
2
votes
1
answer
174
views
1
answer
plotMD plot change plot title
edger plotmd written 18 days ago by mictadlo • 0 • updated 18 days ago by Gordon Smyth ♦ 31k
0
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1
answer
198
views
1
answer
How to use topGO and KEGG with de-novo species
limma topgo edger kegg kegga written 18 days ago by mictadlo • 0 • updated 18 days ago by Gordon Smyth ♦ 31k
3
votes
1
answer
96
views
1
answer
Examples of concise description of NGS and bioinformatics (with DESEq2 or edgeR) in M&M of biological paper
edger deseq2 written 19 days ago by Vladimir Krasikov • 90 • updated 19 days ago by Gordon Smyth ♦ 31k
1
vote
1
answer
196
views
1
answer
Length of 'group' must equal number of columns in 'counts'
edger htseqcounts written 20 days ago by mictadlo • 0 • updated 20 days ago by Gordon Smyth ♦ 31k
3
votes
1
answer
240
views
1
answer
read counts for each gene for edgeR
edger htseqcounts written 21 days ago by mictadlo • 0 • updated 21 days ago by Gordon Smyth ♦ 31k
2
votes
1
answer
252
views
1
answer
plotMDS axis labels for limma/EdgeR: PCA or PCoA
limma edger written 21 days ago by andrew.lonsdale • 0 • updated 21 days ago by Gordon Smyth ♦ 31k
2
votes
1
answer
221
views
1
answer
DESeq2 comparing differential expression results
edger deseq2 written 22 days ago by rrcutler • 30 • updated 22 days ago by Michael Love ♦ 13k
11
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3
answers
456
views
3
answers
edgeR - MDS Plot for Count Data
edger plot mds deg written 5 weeks ago by baus87 • 0
1
vote
1
answer
251
views
1
answer
normalization of POL2 ChIP-seq for the calculation of POL2 Pausing Ratios
normalization edger deseq2 written 27 days ago by Bogdan • 470 • updated 27 days ago by Aaron Lun • 16k
1
vote
1
answer
382
views
1
answer
Why Differential expression results differ with edgeR and limma ?
limma edger R differential gene expression written 4 weeks ago by ghk • 0
2
votes
1
answer
336
views
1
answer
decideTests error with edgeR package
edger R differential gene expression written 4 weeks ago by ghk • 0 • updated 4 weeks ago by Aaron Lun • 16k
3
votes
1
answer
324
views
1
answer
edgeR design between and within subjects
edger design and contrast matrix written 4 weeks ago by b.nota • 290 • updated 4 weeks ago by Aaron Lun • 16k
2
votes
2
answers
370
views
2
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Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq limma geoquery edger rna-seq written 5 weeks ago by hkarakurt • 10 • updated 5 weeks ago by Sean Davis ♦ 20k
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