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Showing :
edgeR
•
reset
2
votes
2
replies
116
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
2 days ago
mohammedtoufiq91
▴ 10
2
votes
3
replies
171
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 8 days ago by
Gordon Smyth
50k • written 8 days ago by
Guillermo
• 0
1
vote
2
replies
221
views
Citation for edgeR user guide
edgeR
written 4 weeks ago by
k___
▴ 30
1
vote
3
replies
279
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 9 days ago by
Gordon Smyth
50k • written 10 days ago by
Ashley
• 0
5
votes
3
replies
327
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
4
votes
2
replies
649
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
21 days ago • updated 17 days ago
gene_bioconductor
▴ 10
0
votes
1
reply
183
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 21 days ago by
Gordon Smyth
50k • written 21 days ago by
z_bahari
• 0
4
votes
6
replies
488
views
FilterByExpr low counts with small sample size
edgeR
5 weeks ago • updated 4 weeks ago
Jonathan
▴ 10
3
votes
3
replies
372
views
permutation test in edgeR
rna-seq
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Netanel
• 0
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 weeks ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
3
replies
225
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
prity6459
• 0
0
votes
2
replies
158
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
4 weeks ago
prity6459
• 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 5 weeks ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
1
vote
3
replies
373
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
286
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
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 11.6 years ago by
Maria Keays
▴ 30
3
votes
5
replies
422
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Fabian
• 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 12.5 years ago by
Bogdan
▴ 670
0
votes
6
replies
379
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Faisal
• 0
5
votes
3
replies
758
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
0
votes
1
reply
261
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
scoops_streams_06
• 0
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
2
votes
2
replies
279
views
between lane normalization upper quantile
EDASeq
edgeR
10 weeks ago • updated 9 weeks ago
elesofi
• 0
0
votes
2
replies
308
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
294
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
549
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
11
replies
811
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
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
1
reply
299
views
ExactTest vs QLFTest
edgeR
updated 11 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
fr8712ca-s
• 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 15 months ago by
Rebekah
• 0
1
vote
6
replies
538
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
12 weeks ago
mico
• 0
5
votes
4
replies
441
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
2
votes
6
replies
450
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago
tsl0026
• 0
3
votes
2
replies
517
views
How does one test for interactions in EdgeR?
edgeR
3 months ago
pl23
• 0
1
vote
2
replies
357
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
3 months ago
mico
• 0
0
votes
4
replies
374
views
Nested paired design
edgeR
3 months ago
manduchi
▴ 10
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
3
votes
4
replies
8.7k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by
Dimitris
• 0 • written 10.9 years ago by
Makis Motakis
▴ 30
1
vote
8
replies
596
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
4
votes
4
replies
467
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
0
votes
5
replies
652
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
4 months ago • updated 3 months ago
Lucy
▴ 60
6
votes
7
replies
621
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
0
votes
0
replies
275
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
401
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
50 results • Page
1 of 1
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered"
by
Michael Love
42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
ATpoint
★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Comment: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
by
jovel_juan
▴ 30
enrichPlot requirements are rather low. All what it needs is to provide few columns named specifically. I student of mine wrote the first v…
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
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