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DeSeq2
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0
votes
1
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40
views
Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 2 hours ago by
ATpoint
★ 5.0k • written 3 hours ago by
js101
• 0
0
votes
0
replies
33
views
How to start learning RNA sequence analysis with DESeq2
DESeq2
21 hours ago
Syed
• 0
1
vote
4
replies
170
views
Bulk RNAseq analysis for
DESeq2
RNASeq
edgeR
limma
2 days ago • updated 1 day 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
153
views
DESeq2 for 16S rRNA Analysis
DESeq2
updated 12 days ago by
James W. MacDonald
68k • written 12 days ago by
lizflor
• 0
0
votes
5
replies
261
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq
DESeq2
DifferentialExpression
updated 15 days ago by
Michael Love
43k • written 15 days ago by
Ahmed Salah
• 0
0
votes
2
replies
207
views
lfc shrinkage estimator in DESeq2
DESeq2
written 15 days ago by
julia_mcdonough
• 0
0
votes
13
replies
843
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 15 days ago by
Gordon Smyth
53k • written 21 days ago by
chp265
• 0
0
votes
6
replies
643
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 22 days ago by
Martin Morgan
25k • written 9 weeks ago by
Benjamin
• 0
0
votes
1
reply
291
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage
DESeq2
contrast
updated 22 days ago by
ATpoint
★ 5.0k • written 25 days ago by
ja569116
• 0
0
votes
1
reply
149
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
413
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
7 weeks ago • updated 25 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 11 weeks ago by
Ahmed Salah
• 0
0
votes
1
reply
247
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 11 weeks ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
Asma
• 0
1
vote
11
replies
2.3k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 11 weeks ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
Raya
• 0
0
votes
2
replies
413
views
DESeq2 on non-RNASeq counts data
DESeq2
written 5 months ago by
vs
• 0
0
votes
2
replies
394
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
0
replies
195
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 12 weeks ago by
Kevin Blighe
★ 4.0k • written 3 months ago by
colinmccornack
• 0
0
votes
4
replies
339
views
Getting a large intercept with DESeq2
DESeq2
DifferentialExpression
TimeCourse
12 weeks ago
Denise
• 0
0
votes
2
replies
378
views
Setting up a DESeq2 Design with Paired Data
DESeq2
3 months ago
Alexander
• 0
2
votes
4
replies
586
views
DESeq2 interactions
DESeq2
updated 3 months ago by
Michael Love
43k • written 4 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
443
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
894
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 6.5 years ago by
lim6432
▴ 60
0
votes
11
replies
823
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
5 months ago
Denise
• 0
2
votes
6
replies
691
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
364
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 6 months ago by
Erika
• 0
1
vote
2
replies
553
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
611
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
4.0k
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 7 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
680
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
498
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
668
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
2
replies
2.1k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
9 months ago • updated 8 months ago
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: Subsetting data verses contrasts [DESeq2]?
by
ATpoint
★ 5.0k
This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …
Comment: Bulk RNAseq analysis for
by
Mariami
• 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: Bulk RNAseq analysis for
by
Mariami
• 0
Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…
Answer: Bulk RNAseq analysis for
by
Gordon Smyth
53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Answer: Bulk RNAseq analysis for
by
James W. MacDonald
68k
In my experience, the within-clone variability of differentiated stem cells is often as large or larger than the between-clone variability,…
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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