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DeSeq2
•
reset
0
votes
3
replies
140
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
written 6 days ago by
ja569116
• 0
0
votes
2
replies
220
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 20 days ago by
Michael Love
43k • written 22 days ago by
Benjamin
• 0
3
votes
6
replies
901
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 5 weeks ago by
Ahmed Salah
• 0
0
votes
1
reply
165
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 25 days ago by
ATpoint
★ 5.0k • written 26 days ago by
Junmo
• 0
0
votes
2
replies
1.1k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Asma
• 0
1
vote
11
replies
1.8k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 4 weeks ago by
Kevin Blighe
★ 4.0k • written 4 months ago by
Raya
• 0
0
votes
2
replies
311
views
DESeq2 on non-RNASeq counts data
DESeq2
updated 4 days ago by
TikTsokaasocissalpc
• 0 • written 4 months ago by
vs
• 0
0
votes
2
replies
336
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
updated 5 weeks ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
gogeni5529
• 0
0
votes
0
replies
136
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 5 weeks ago by
Kevin Blighe
★ 4.0k • written 6 weeks ago by
colinmccornack
• 0
0
votes
4
replies
224
views
Getting a large intercept with DESeq2
DESeq2
DifferentialExpression
TimeCourse
5 weeks ago
Denise
• 0
0
votes
2
replies
241
views
Setting up a DESeq2 Design with Paired Data
DESeq2
7 weeks ago
Alexander
• 0
2
votes
4
replies
503
views
DESeq2 interactions
DESeq2
updated 8 weeks ago by
Michael Love
43k • written 3 months ago by
Michael
• 0
3
votes
14
replies
1.2k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 4 months ago by
Aurélie
• 0
0
votes
3
replies
382
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
yongjie.wang
• 0
0
votes
1
reply
722
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm
DESeq2
updated 3 months ago by
Michael Love
43k • written 4 months ago by
KS
• 0
3
votes
5
replies
1.1k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 3 months ago by
James W. MacDonald
68k • written 4 months ago by
snijesh
▴ 200
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 4 months ago by
James W. MacDonald
68k • written 6.4 years ago by
lim6432
▴ 60
0
votes
11
replies
686
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
4 months ago
Denise
• 0
2
votes
6
replies
621
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
4 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
306
views
DESeq2 inconsistent fits depending on model design with interacting factors
des
DESeq2
written 4 months ago by
fedor.bezrukov
▴ 10
0
votes
4
replies
926
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm
s-value
DESeq2
updated 4 months ago by
Michael Love
43k • written 5 months ago by
Erika
• 0
1
vote
2
replies
430
views
Differential expression on the transcript-level
DESeq2
updated 5 months ago by
swbarnes2
★ 1.4k • written 5 months ago by
泓朴
• 0
3
votes
13
replies
2.2k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 14 months ago by
bioshot.com
• 0
4
votes
8
replies
2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2
edgeR
limma
xenium
Voom
5 months ago
richardallenfriedmanbrooklyn
▴ 30
7
votes
9
replies
5.7k
views
competitive enrichment test yields too few significant results, self-contained too many
limma
DESeq2
fry
edgeR
5 months ago
bbao
▴ 10
0
votes
1
reply
552
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport
DESeq2
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
IUH
• 0
0
votes
2
replies
1.0k
views
gene detection across experiments
DESeq2
Normalization
5 months ago
Mara
• 0
5
votes
11
replies
3.4k
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
written 7 months ago by
caroline.zanchi
▴ 10
1
vote
5
replies
4.8k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 5 months ago by
Michael Love
43k • written 6 months ago by
Alexander
• 0
1
vote
1
reply
2.2k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2
multifactorialdesign
interaction
InteractionSet
updated 6 months ago by
Michael Love
43k • written 6 months ago by
Integrative
• 0
0
votes
2
replies
1.2k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 6 months ago by
Michael Love
43k • written 6 months ago by
Rocio
• 0
3
votes
2
replies
1.5k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
written 6 months ago by
Christian
▴ 20
1
vote
2
replies
2.7k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 6 months ago by
corranna98
• 0
3
votes
1
reply
3.8k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 6 months ago by
Michael Love
43k • written 6 months ago by
Chenghao
▴ 10
0
votes
1
reply
622
views
DESeq2 results
result
DESeq2
subsetting
updated 6 months ago by
ATpoint
★ 5.0k • written 6 months ago by
rajdeepboral00
• 0
0
votes
1
reply
442
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 6 months ago by
Michael Love
43k • written 7 months ago by
Pak
• 0
0
votes
1
reply
608
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
updated 7 months ago by
Michael Love
43k • written 7 months ago by
s.malik
• 0
3
votes
2
replies
2.1k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
7 months ago
dudutchy
▴ 10
2
votes
3
replies
1.5k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR
DESeq2
haplotype
limma
7 months ago
Paulito
• 0
4
votes
4
replies
2.1k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2
ComplexHeatmap
7 months ago
caroline.zanchi
▴ 10
0
votes
1
reply
444
views
DESeq2 from phyloseq error
DESeq2
phyloseq
7 months ago
asafpr
• 0
3
votes
1
reply
669
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2
apeglm
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
sk
• 0
1
vote
5
replies
1.5k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2
heatmaps
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
caroline.zanchi
▴ 10
8
votes
3
replies
3.1k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 6 months ago by
Michael Love
43k • written 7 months ago by
Cassia
▴ 40
2
votes
4
replies
1.9k
views
Filtering after DESeq
DESeq2
IHW
written 8 months ago by
caroline.zanchi
▴ 10
0
votes
4
replies
1.2k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
7 months ago
sk
• 0
0
votes
6
replies
1.8k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
8 months ago • updated 7 months ago
AMgroup
• 0
0
votes
2
replies
748
views
Design formula for circadian time-course data for vst() function
DESeq2
8 months ago
Vishnu
• 0
0
votes
2
replies
888
views
Analyzing TnSeq data with DESeq2
DESeq2
written 8 months ago by
newfunland
• 0
0
votes
1
reply
1.2k
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2
RUVSeq
updated 8 months ago by
Michael Love
43k • written 9 months ago by
Simran
• 0
4,842 results • Page
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Comment: nice 3D displays for PCA analysis
by
adam80haynes
• 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital
by
TikTsokaasocissalpc
• 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
TikTsokaasocissalpc
• 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers
by
Gordon Smyth
53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Answer: wgcna module preseravtion taking too long?
by
ATpoint
★ 5.0k
WGCNA is not a Bioconductor package, you won't get an answer here. Consider biostars.org or the r/bioinformatics reddit. Note that 10 sampl…
Votes
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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Gordon Smyth
53k
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Hervé Pagès
16k
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to
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6.7k
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to
Istvan Albert
▴ 50
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Dario Strbenac
★ 1.6k
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