Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Deseq2
•
reset
0
votes
2
replies
71
views
Subsetting DDS object for individual conditions over time
DESeq2
1 day ago • updated 10 hours ago
A
▴ 60
1
vote
1
reply
236
views
Subsetting data verses contrasts [DESeq2]?
DESeq2
updated 23 days ago by
ATpoint
★ 5.0k • written 23 days ago by
js101
• 0
0
votes
0
replies
109
views
How to start learning RNA sequence analysis with DESeq2
DESeq2
24 days ago
Syed
• 0
1
vote
4
replies
410
views
Bulk RNAseq analysis for
DESeq2
RNASeq
edgeR
limma
25 days ago • updated 24 days ago
Mariami
• 0
0
votes
5
replies
2.3k
views
DESeq2 contrast cleaning problem
software error
bugs
deseq2
written 10.1 years ago by
john.hu
• 0
0
votes
1
reply
203
views
DESeq2 for 16S rRNA Analysis
DESeq2
updated 5 weeks ago by
James W. MacDonald
68k • written 5 weeks ago by
lizflor
• 0
0
votes
5
replies
312
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq
DESeq2
DifferentialExpression
updated 5 weeks ago by
Michael Love
43k • written 5 weeks ago by
Ahmed Salah
▴ 10
0
votes
2
replies
263
views
lfc shrinkage estimator in DESeq2
DESeq2
written 5 weeks ago by
julia_mcdonough
• 0
0
votes
13
replies
967
views
Making a Full Rank Model for Allele-Specific Expression with DESeq2
DESeq2
updated 5 weeks ago by
Gordon Smyth
53k • written 6 weeks ago by
chp265
• 0
0
votes
6
replies
789
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 6 weeks ago by
Martin Morgan
25k • written 3 months ago by
Benjamin
• 0
0
votes
1
reply
380
views
DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage
DESeq2
contrast
updated 6 weeks ago by
ATpoint
★ 5.0k • written 7 weeks ago by
ja569116
• 0
0
votes
1
reply
197
views
News:
Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano
GSEABase
pheatmap
Workshop
DESeq2
written 7 weeks ago by
Frances Turner
▴ 20
0
votes
3
replies
514
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
11 weeks ago • updated 7 weeks ago
ja569116
• 0
6
votes
6
replies
1.3k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq
DESeq2
DifferentialExpression
RNASeqData
written 3 months ago by
Ahmed Salah
▴ 10
0
votes
1
reply
293
views
Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 3 months ago by
ATpoint
★ 5.0k • written 3 months ago by
Junmo
• 0
0
votes
2
replies
1.3k
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 7 months ago by
Asma
• 0
1
vote
11
replies
2.7k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2
scRNAseq
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 6 months ago by
Raya
• 0
0
votes
2
replies
467
views
DESeq2 on non-RNASeq counts data
DESeq2
written 6 months ago by
vs
• 0
0
votes
2
replies
424
views
3-factor DESeq2 trime-series analysis
time-series
DESeq2
updated 3 months ago by
Kevin Blighe
★ 4.0k • written 5 months ago by
gogeni5529
• 0
0
votes
1
reply
292
views
[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
3 months ago • updated 22 days ago
colinmccornack
• 0
0
votes
4
replies
394
views
Getting a large intercept with DESeq2
DESeq2
DifferentialExpression
TimeCourse
3 months ago
Denise
• 0
0
votes
2
replies
483
views
Setting up a DESeq2 Design with Paired Data
DESeq2
4 months ago • updated 3 months ago
Alexander
• 0
2
votes
4
replies
651
views
DESeq2 interactions
DESeq2
updated 4 months ago by
Michael Love
43k • written 5 months ago by
Michael
• 0
3
votes
14
replies
1.6k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 7 months ago by
Aurélie
• 0
0
votes
3
replies
489
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 6 months ago by
yongjie.wang
• 0
0
votes
1
reply
1.1k
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 6 months ago by
KS
• 0
3
votes
5
replies
1.3k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 6 months ago by
James W. MacDonald
68k • written 6 months ago by
snijesh
▴ 200
17
votes
45
replies
14k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 6 months ago by
James W. MacDonald
68k • written 6.6 years ago by
lim6432
▴ 60
0
votes
11
replies
903
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
6 months ago
Denise
• 0
2
votes
6
replies
737
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
6 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
419
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
1.2k
views
Using shrunken LFC and s-value from DESeq2 as DGE results
apeglm
s-value
DESeq2
updated 7 months ago by
Michael Love
43k • written 7 months ago by
Erika
• 0
1
vote
2
replies
620
views
Differential expression on the transcript-level
DESeq2
updated 7 months ago by
swbarnes2
★ 1.4k • written 7 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 17 months ago by
bioshot.com
• 0
4
votes
8
replies
2.2k
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
6.0k
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
658
views
discrepancy in IDs from file and tx2gene (IDs don't match)
tximport
DESeq2
updated 7 months ago by
James W. MacDonald
68k • written 8 months ago by
IUH
• 0
0
votes
2
replies
1.1k
views
gene detection across experiments
DESeq2
Normalization
8 months ago
Mara
• 0
5
votes
11
replies
4.4k
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
written 10 months ago by
caroline.zanchi
▴ 10
1
vote
5
replies
5.7k
views
Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low counts and dropouts produce interesting volcano plots.
DESeq2
updated 7 months ago by
Michael Love
43k • written 9 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 8 months ago by
Michael Love
43k • written 8 months ago by
Integrative
• 0
0
votes
2
replies
1.4k
views
6 groups to compare DESeq2 (Wald vs LRT)
DESeq2
updated 8 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 9 months ago by
Christian
▴ 20
1
vote
2
replies
2.8k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 9 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 9 months ago by
Michael Love
43k • written 9 months ago by
Chenghao
▴ 10
0
votes
1
reply
696
views
DESeq2 results
result
DESeq2
subsetting
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
rajdeepboral00
• 0
0
votes
1
reply
527
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 9 months ago by
Michael Love
43k • written 9 months ago by
Pak
• 0
0
votes
1
reply
703
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
updated 9 months ago by
Michael Love
43k • written 9 months ago by
s.malik
• 0
3
votes
3
replies
2.3k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
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
9 months ago
Paulito
• 0
4,852 results • Page
1 of 98
Recent ...
Replies
Comment: Subsetting DDS object for individual conditions over time
by
A
▴ 60
Hi @atpoint Thank you for the quick reply! and this makes sense! I will confirm with a corr to see how the SFs differ but also how DE dif…
Answer: Subsetting DDS object for individual conditions over time
by
ATpoint
★ 5.0k
It would surprise my quite a bit if the size factors would differ notably between subset or not. I would always try to keep the size factor…
Comment: GSEA error
by
Adithi
• 0
Thank you so much. That makes perfect sense to me. I will work on this.
Comment: tximeta cannot open annotation gtf?
by
Michael Love
43k
Yes, so this is the same type of error you would get if you tried to assemble a *SummarizedExperiment* manually with tximport + GTF process…
Answer: tximeta cannot open annotation gtf?
by
ATpoint
★ 5.0k
> Timeout of 60 seconds was reached You have to increase the default timeout limits for downloads, `options(timeout=3600)`. GENCODE serve…
Votes
Answer: RNA Seq using Lrt
Answer: DESeq2 LRT Reduced Formula
Answer: DESeq2: LRT or WALD guidance
Answer: GSEA error
Answer: OrgDb for maize
Awards
• All
Popular Question
to
A
▴ 60
Popular Question
to
Aichatou
• 0
Popular Question
to
boczniak767
▴ 740
Popular Question
to
shepherl
4.3k
Popular Question
to
Gordon Smyth
53k
Locations
• All
China,
1 hour ago
WEHI, Melbourne, Australia,
1 hour ago
China,
2 hours ago
China,
3 hours ago
Poland,
3 hours ago
Traffic: 970 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6