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edger
•
reset
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 29 days ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2
limma
edger
permutation
updated 5 months ago by
Gordon Smyth
50k • written 8.2 years ago by
Radek
▴ 90
7
votes
2
replies
859
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
6
votes
2
replies
742
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
10 months ago
Josué
▴ 20
6
votes
7
replies
968
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 6 months ago by
ATpoint
★ 4.1k • written 7 months ago by
jonas.freimuth
▴ 20
6
votes
7
replies
600
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
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 28 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
5
votes
3
replies
304
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 days ago by
Gordon Smyth
50k • written 29 days ago by
Shaimaa Gamal
• 0
5
votes
2
replies
599
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
5
votes
4
replies
425
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago
pl23
• 0
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 8 months ago by
Novice_cam
• 0 • written 6.5 years ago by
knaxerova
▴ 10
5
votes
6
replies
456
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 4 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
nhaus
▴ 30
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 4 months ago by
Shaimaa Gamal
• 0 • written 7.2 years ago by
myprogramming2016
• 0
5
votes
3
replies
734
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Jack S.
▴ 50
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
4
votes
12
replies
3.8k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 7 months ago by
Miguel
• 0 • written 3.2 years ago by
robert.chen
• 0
4
votes
6
replies
465
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 25 days ago
Jonathan
▴ 10
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 3.6 years ago by
ATpoint
★ 4.1k
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
9 months ago
Luca
• 0
4
votes
2
replies
619
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
14 days ago • updated 11 days ago
gene_bioconductor
▴ 10
4
votes
4
replies
455
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by
James W. MacDonald
65k • written 4 months ago by
Geo
• 0
4
votes
2
replies
671
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
alvaroperona1
▴ 10
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 8 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
4
votes
3
replies
1.1k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
garcia
• 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
4 months ago
Luca
• 0
3
votes
3
replies
568
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
8 months ago
Nisha
• 0
3
votes
5
replies
412
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Fabian
• 0
3
votes
2
replies
494
views
How does one test for interactions in EdgeR?
edgeR
3 months ago
pl23
• 0
3
votes
2
replies
688
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod
RNASeqData
edgeR
DESeq2
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
CDSPARKS
▴ 10
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR
RnaSeqSampleSizeData
RNAseq
updated 4 months ago by
Gordon Smyth
50k • written 3.0 years ago by
Lucy
▴ 60
3
votes
6
replies
858
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
3
votes
3
replies
709
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 4 months ago by
Jurgen
• 0
3
votes
3
replies
589
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression
edgeR
limma
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
stuartthafass
• 0
3
votes
4
replies
503
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Jack S.
▴ 50
3
votes
3
replies
367
views
permutation test in edgeR
rna-seq
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 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
2
votes
2
replies
288
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
9 weeks ago
Sabiha
▴ 20
2
votes
3
replies
309
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
JKim
• 0
2
votes
4
replies
645
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
2
votes
6
replies
437
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago • updated 12 weeks ago
tsl0026
• 0
2
votes
2
replies
2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger
deseq2
updated 8 months ago by
marjim
• 0 • written 6.4 years ago by
nyoungb2
• 0
2
votes
3
replies
386
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
3
replies
837
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 9 months ago by
Vitor
• 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 14 months ago by
Rebekah
• 0
2
votes
1
reply
613
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR
DESeq2
updated 11 months ago by
ATpoint
★ 4.1k • written 11 months ago by
calvincornell1996
• 0
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 11 months ago
Luis
• 0
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 8 months ago by
lucap
• 0 • written 3.1 years ago by
Marianna
▴ 20
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
10 months ago • updated 9 months ago
mohammedtoufiq91
▴ 10
2
votes
3
replies
109
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 2 days ago by
Guillermo
• 0
50 results • Page
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Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters
by
anne-laure
• 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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