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Showing :
DEseq2
•
reset
6
votes
11
replies
3.7k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 17 days ago by
Priya
• 0 • written 3.1 years ago by
Marina
▴ 40
0
votes
2
replies
1.4k
views
DE genes over time with DESeq2
deseq2
timecourse
design and contrast matrix
updated 21 days ago by
ta_awwad
▴ 10 • written 8.4 years ago by
Assa Yeroslaviz
★ 1.5k
4
votes
4
replies
1.0k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 13 days ago by
feather-W
• 0 • written 11 months ago by
Bernardo
▴ 10
4
votes
7
replies
755
views
weird volcano plot
DESeq2
updated 22 days ago by
Shuning
• 0 • written 4 months ago by
shouzheng
▴ 10
4
votes
7
replies
613
views
DESeq2 unable to handle large count values
DESeq2
updated 9 days ago by
Michael Love
41k • written 4 months ago by
robennet
• 0
0
votes
13
replies
580
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2
SmallRNA
updated 29 days ago by
Michael Love
41k • written 5 weeks ago by
r.r.bioinf
• 0
3
votes
5
replies
543
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 24 days ago by
Michael Love
41k • written 4 weeks ago by
sap275
▴ 10
0
votes
2
replies
399
views
help checking the design matrix and contrast in DESeq2 "not full rank" scenario
DESeq2
6 weeks ago • updated 29 days ago
ccshao
▴ 70
0
votes
4
replies
354
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 14 days ago by
Michael Love
41k • written 14 days ago by
Jad
• 0
0
votes
7
replies
339
views
DESeq2 filtering vs edgeR filtering
DESeq2
15 days ago • updated 2 days ago
fr8712ca-s
• 0
1
vote
3
replies
315
views
DEseq2 coefficient
DESeq2
coefficient
4 weeks ago • updated 12 days ago
JKim
• 0
0
votes
3
replies
306
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 8 weeks ago by
pl23
• 0
0
votes
8
replies
294
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
21 days ago
michelafrancesconi8
• 0
0
votes
2
replies
293
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 26 days ago by
ATpoint
★ 4.0k • written 28 days ago by
Suvi
• 0
0
votes
2
replies
272
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
21 days ago • updated 19 days ago
Viktor Thiel
• 0
2
votes
6
replies
266
views
Factor vs Character in design
DESeq2
22 days ago
James Aiden
• 0
1
vote
4
replies
265
views
Further clarification of unbalanced group sizes DESeq2
DESeq2
28 days ago • updated 27 days ago
hmillike
• 0
1
vote
3
replies
259
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 24 days ago by
swbarnes2
★ 1.3k • written 27 days ago by
sap275
▴ 10
0
votes
2
replies
247
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 14 days ago by
Michael Love
41k • written 16 days ago by
gglatzer
• 0
1
vote
3
replies
245
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2
glmGamPoi
28 days ago • updated 22 days ago
I-Hsuan Lin
▴ 10
1
vote
4
replies
234
views
DESeq2 Replicates
DESeq2
RNASeq
22 days ago
kcarey
• 0
0
votes
3
replies
225
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 24 days ago by
James W. MacDonald
65k • written 27 days ago by
MEME
▴ 10
1
vote
3
replies
225
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 7 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
221
views
DEseq2 dispersion plot
DESeq2
updated 23 days ago by
Michael Love
41k • written 28 days ago by
Emma
• 0
2
votes
1
reply
191
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 16 days ago by
ATpoint
★ 4.0k • written 16 days ago by
hemantcnaik
• 0
0
votes
1
reply
191
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2
pheatmap
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
zhangaimei
• 0
0
votes
3
replies
178
views
Help with Complex DESeq2 Design
DESeq2
updated 8 days ago by
ATpoint
★ 4.0k • written 10 days ago by
kelsey.beavers
• 0
1
vote
1
reply
166
views
i'm not getting any differentially expressed genes.
DESeq2
updated 16 days ago by
ATpoint
★ 4.0k • written 16 days ago by
Marilyn
• 0
0
votes
2
replies
161
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
15 days ago • updated 14 days ago
kcarey
• 0
2
votes
2
replies
161
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
13 days ago • updated 11 days ago
feather-W
• 0
0
votes
3
replies
160
views
PCA of different bacterial species
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Laura
▴ 10
1
vote
1
reply
160
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 17 days ago by
ATpoint
★ 4.0k • written 18 days ago by
synat.keam
• 0
0
votes
1
reply
150
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 21 days ago by
ATpoint
★ 4.0k • written 21 days ago by
Sneha
• 0
0
votes
1
reply
144
views
few significant genes from DESeq2 analysis
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Ming
• 0
0
votes
1
reply
136
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 21 days ago by
ATpoint
★ 4.0k • written 21 days ago by
daiane.hemerichbrennan
• 0
1
vote
2
replies
134
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
7 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
133
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
8 days ago • updated 7 days ago
kcarey
• 0
1
vote
1
reply
122
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 10 days ago by
Michael Love
41k • written 11 days ago by
Emma
• 0
0
votes
1
reply
120
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 10 days ago by
Michael Love
41k • written 11 days ago by
Yuqin
• 0
3
votes
2
replies
118
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
3 days ago
Anita
▴ 10
0
votes
1
reply
101
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 10 days ago by
Michael Love
41k • written 10 days ago by
rahaf.nazzal9
• 0
0
votes
1
reply
88
views
collapseReplicates dimension error
DESeq2
Dese
updated 2 days ago by
Michael Love
41k • written 6 days ago by
Léa
• 0
0
votes
1
reply
24
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 3 hours ago by
Michael Love
41k • written 4 hours ago by
Mikushi
• 0
43 results • Page
1 of 1
Recent ...
Replies
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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James W. MacDonald
65k
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Pierre Lindenbaum
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Gordon Smyth
50k
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