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Showing :
edgeR
•
reset
2
votes
2
replies
115
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
2 days ago • updated 1 day ago
mohammedtoufiq91
▴ 10
2
votes
3
replies
167
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
Guillermo
• 0
1
vote
3
replies
274
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 8 days ago by
Gordon Smyth
50k • written 9 days ago by
Ashley
• 0
0
votes
1
reply
182
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 20 days ago by
Gordon Smyth
50k • written 20 days ago by
z_bahari
• 0
4
votes
2
replies
648
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
20 days ago • updated 16 days ago
gene_bioconductor
▴ 10
1
vote
2
replies
217
views
Citation for edgeR user guide
edgeR
written 29 days ago by
k___
▴ 30
4
votes
6
replies
487
views
FilterByExpr low counts with small sample size
edgeR
5 weeks ago • updated 4 weeks ago
Jonathan
▴ 10
0
votes
2
replies
154
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
4 weeks ago
prity6459
• 0
0
votes
3
replies
219
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
prity6459
• 0
5
votes
3
replies
325
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 13 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Shaimaa Gamal
• 0
3
votes
3
replies
371
views
permutation test in edgeR
rna-seq
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Netanel
• 0
1
vote
3
replies
371
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Simran
• 0
5
votes
6
replies
466
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 5 weeks ago by
ATpoint
★ 4.2k • written 6 weeks ago by
nhaus
▴ 40
1
vote
3
replies
285
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 6 weeks ago by
James W. MacDonald
66k • written 6 weeks ago by
Shaimaa Gamal
• 0
0
votes
2
replies
201
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
7 weeks ago
Marianna
▴ 20
0
votes
4
replies
450
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
7 weeks ago
Lucy
▴ 60
3
votes
5
replies
420
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Fabian
• 0
0
votes
6
replies
378
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Faisal
• 0
0
votes
1
reply
260
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
scoops_streams_06
• 0
5
votes
3
replies
757
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
Jack S.
▴ 50
2
votes
3
replies
317
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
JKim
• 0
0
votes
2
replies
307
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
z_bahari
• 0
2
votes
2
replies
279
views
between lane normalization upper quantile
EDASeq
edgeR
9 weeks ago
elesofi
• 0
2
votes
2
replies
293
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
10 weeks ago
Sabiha
▴ 20
1
vote
3
replies
448
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
3
votes
4
replies
545
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Jack S.
▴ 50
0
votes
1
reply
244
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
Fabian
• 0
0
votes
11
replies
807
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 11 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
mico
• 0
0
votes
1
reply
298
views
ExactTest vs QLFTest
edgeR
updated 11 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
fr8712ca-s
• 0
1
vote
6
replies
537
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
12 weeks ago
mico
• 0
2
votes
6
replies
448
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago
tsl0026
• 0
5
votes
4
replies
440
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago
pl23
• 0
0
votes
8
replies
693
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago
Marianna
▴ 20
3
votes
2
replies
515
views
How does one test for interactions in EdgeR?
edgeR
3 months ago
pl23
• 0
0
votes
4
replies
372
views
Nested paired design
edgeR
3 months ago
manduchi
▴ 10
1
vote
2
replies
356
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
3 months ago
mico
• 0
2
votes
3
replies
398
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
Shaimaa Gamal
• 0
4
votes
4
replies
465
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by
James W. MacDonald
66k • written 4 months ago by
Geo
• 0
6
votes
7
replies
619
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
aa.machado001
• 0
1
vote
8
replies
591
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
sat
• 0
0
votes
0
replies
274
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
4 months ago
Jawahar
• 0
2
votes
4
replies
665
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
4 months ago
Sabiha
▴ 20
0
votes
3
replies
400
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annasoudi
• 0
3
votes
3
replies
742
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
Jurgen
• 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
4 months ago
Luca
• 0
0
votes
1
reply
328
views
download problem
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
theokirkland3
• 0
0
votes
5
replies
652
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
4 months ago • updated 3 months ago
Lucy
▴ 60
1
vote
2
replies
502
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
5 months ago
Sabiha
▴ 20
5
votes
2
replies
612
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
1
vote
2
replies
470
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
Jurgen
• 0
50 results • Page
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Comment: Not able to install any Bioconductor 3.18 package [unable to access index]
by
merv
▴ 120
Thanks! I can confirm it is working now - had been broken since sometime yesterday.
Comment: Errors in chromosome annotation-biomaRt
by
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▴ 40
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by
James W. MacDonald
66k
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by
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• 0
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Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
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3.9k
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Votes
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Seurat/DESeq2 - single cell RNA-seq differential expression
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