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DESeq2
•
reset
1
vote
1
reply
101
views
Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 2 days ago by
ATpoint
★ 5.0k • written 2 days ago by
js101
• 0
0
votes
0
replies
67
views
How to start learning RNA sequence analysis with DESeq2
DESeq2
3 days ago
Syed
• 0
1
vote
4
replies
283
views
Bulk RNAseq analysis for
DESeq2
RNASeq
edgeR
limma
4 days ago • updated 3 days ago
Mariami
• 0
0
votes
5
replies
2.3k
views
DESeq2 contrast cleaning problem
software error
bugs
deseq2
written 10.0 years ago by
john.hu
• 0
0
votes
1
reply
166
views
DESeq2 for 16S rRNA Analysis
DESeq2
updated 14 days ago by
James W. MacDonald
68k • written 15 days ago by
lizflor
• 0
0
votes
5
replies
278
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq
DESeq2
DifferentialExpression
updated 17 days ago by
Michael Love
43k • written 17 days ago by
Ahmed Salah
• 0
0
votes
2
replies
214
views
lfc shrinkage estimator in DESeq2
DESeq2
written 18 days ago by
julia_mcdonough
• 0
0
votes
13
replies
866
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 18 days ago by
Gordon Smyth
53k • written 24 days ago by
chp265
• 0
0
votes
6
replies
665
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 25 days ago by
Martin Morgan
25k • written 10 weeks ago by
Benjamin
• 0
0
votes
1
reply
305
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage
DESeq2
contrast
updated 24 days ago by
ATpoint
★ 5.0k • written 28 days ago by
ja569116
• 0
0
votes
1
reply
155
views
News:
Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano
GSEABase
pheatmap
Workshop
DESeq2
written 4 weeks ago by
Frances Turner
▴ 20
0
votes
3
replies
426
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
8 weeks ago • updated 28 days ago
ja569116
• 0
3
votes
6
replies
1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 12 weeks ago by
Ahmed Salah
• 0
0
votes
1
reply
255
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 10 weeks ago by
ATpoint
★ 5.0k • written 10 weeks ago by
Junmo
• 0
0
votes
2
replies
1.3k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 12 weeks ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
Asma
• 0
1
vote
11
replies
2.4k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 12 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Raya
• 0
0
votes
2
replies
415
views
DESeq2 on non-RNASeq counts data
DESeq2
written 5 months ago by
vs
• 0
0
votes
2
replies
398
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
updated 12 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
gogeni5529
• 0
0
votes
1
reply
239
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
3 months ago • updated 1 day ago
colinmccornack
• 0
0
votes
4
replies
348
views
Getting a large intercept with DESeq2
DESeq2
DifferentialExpression
TimeCourse
3 months ago • updated 12 weeks ago
Denise
• 0
0
votes
2
replies
402
views
Setting up a DESeq2 Design with Paired Data
DESeq2
3 months ago
Alexander
• 0
2
votes
4
replies
594
views
DESeq2 interactions
DESeq2
updated 3 months ago by
Michael Love
43k • written 5 months ago by
Michael
• 0
3
votes
14
replies
1.5k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 6 months ago by
Aurélie
• 0
0
votes
3
replies
448
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq
DESeq2
updated 5 months ago by
Michael Love
43k • written 5 months ago by
yongjie.wang
• 0
0
votes
1
reply
913
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm
DESeq2
updated 5 months ago by
Michael Love
43k • written 5 months ago by
KS
• 0
3
votes
5
replies
1.2k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 5 months ago by
James W. MacDonald
68k • written 5 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 5 months ago by
James W. MacDonald
68k • written 6.6 years ago by
lim6432
▴ 60
0
votes
11
replies
831
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
6 months ago • updated 5 months ago
Denise
• 0
2
votes
6
replies
695
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
368
views
DESeq2 inconsistent fits depending on model design with interacting factors
des
DESeq2
written 6 months ago by
fedor.bezrukov
▴ 10
0
votes
4
replies
1.1k
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm
s-value
DESeq2
updated 6 months ago by
Michael Love
43k • written 7 months ago by
Erika
• 0
1
vote
2
replies
560
views
Differential expression on the transcript-level
DESeq2
updated 6 months ago by
swbarnes2
★ 1.4k • written 6 months ago by
泓朴
• 0
3
votes
13
replies
2.4k
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 16 months ago by
bioshot.com
• 0
4
votes
8
replies
2.1k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2
edgeR
limma
xenium
Voom
7 months ago
richardallenfriedmanbrooklyn
▴ 30
7
votes
9
replies
5.9k
views
competitive enrichment test yields too few significant results, self-contained too many
limma
DESeq2
fry
edgeR
7 months ago
bbao
▴ 10
0
votes
1
reply
617
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport
DESeq2
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
IUH
• 0
0
votes
2
replies
1.1k
views
gene detection across experiments
DESeq2
Normalization
7 months ago
Mara
• 0
5
votes
11
replies
4.1k
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
written 9 months ago by
caroline.zanchi
▴ 10
1
vote
5
replies
5.4k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 6 months ago by
Michael Love
43k • written 8 months ago by
Alexander
• 0
1
vote
1
reply
2.3k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2
multifactorialdesign
interaction
InteractionSet
updated 7 months ago by
Michael Love
43k • written 7 months ago by
Integrative
• 0
0
votes
2
replies
1.3k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 7 months ago by
Michael Love
43k • written 8 months ago by
Rocio
• 0
3
votes
2
replies
1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
written 8 months ago by
Christian
▴ 20
1
vote
2
replies
2.8k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 8 months ago by
corranna98
• 0
3
votes
1
reply
3.9k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Chenghao
▴ 10
0
votes
1
reply
685
views
DESeq2 results
result
DESeq2
subsetting
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
rajdeepboral00
• 0
0
votes
1
reply
503
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Pak
• 0
0
votes
1
reply
673
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
updated 8 months ago by
Michael Love
43k • written 9 months ago by
s.malik
• 0
3
votes
3
replies
2.2k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
updated 2 days ago by
a2a2ddrhaa
• 0 • written 9 months ago by
dudutchy
▴ 10
2
votes
3
replies
1.7k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR
DESeq2
haplotype
limma
8 months ago
Paulito
• 0
4
votes
4
replies
2.2k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2
ComplexHeatmap
8 months ago
caroline.zanchi
▴ 10
4,851 results • Page
1 of 98
Recent ...
Replies
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
by
Gordon Smyth
53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa?
by
Gordon Smyth
53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
by
Korneel
• 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics
by
yesquokkan
• 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2
by
colinmccornack
• 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Votes
Answer: Subsetting data verses contrasts [DESeq2]?
A: WGCNA differences two groups 10 replicates each group
A: WGCNA sample size minimum: why?
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
Answer: Can you colour dendrogram branch clusters in pheatmap?
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