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
0
replies
21
views
PCA plot suggestions
DESeq2
PCAtools
8 hours ago
Aaliya
• 0
0
votes
1
reply
69
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 15 hours ago by
Michael Love
41k • written 18 hours ago by
kcarey
• 0
1
vote
3
replies
83
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 hours ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
0
votes
2
replies
82
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
1 day ago • updated 4 hours ago
winwater0928
• 0
2
votes
1
reply
163
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
0
votes
8
replies
198
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 6 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
3
votes
3
replies
154
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
0
votes
1
reply
88
views
rlog transformation
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ishij9717
• 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 7 days ago by
09191919
• 0
0
votes
1
reply
96
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ussarizona
• 0
0
votes
1
reply
112
views
covariate with negative and positive values
DESeq2
updated 6 days ago by
Michael Love
41k • written 8 days ago by
Brynn
• 0
0
votes
1
reply
112
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 7 days ago by
ATpoint
★ 4.0k • written 7 days ago by
quanah.hudson
• 0
0
votes
4
replies
194
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 days ago • updated 5 days ago
lonn
• 0
0
votes
3
replies
174
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
218
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 6 days ago by
Michael Love
41k • written 10 days ago by
Rajat
• 0
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 10 days ago by
ATpoint
★ 4.0k • written 11 days ago by
Sahar
• 0
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
12 days ago
hemantcnaik
• 0
0
votes
1
reply
117
views
Bioinformatics student
Des
DESeq2
updated 12 days ago by
hemantcnaik
• 0 • written 12 days ago by
Sahar
• 0
0
votes
1
reply
155
views
DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago
Shefali
• 0
0
votes
2
replies
192
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 15 days ago by
Michael Love
41k • written 20 days ago by
nhaus
▴ 30
0
votes
1
reply
138
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 15 days ago by
Michael Love
41k • written 15 days ago by
Adelaide
• 0
0
votes
2
replies
220
views
Regressing out batch effects
DESeq2
updated 15 days ago by
Michael Love
41k • written 20 days ago by
kys91240
• 0
0
votes
2
replies
142
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
152
views
DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
Hong Thu
• 0
1
vote
6
replies
401
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 21 days ago by
Michael Love
41k • written 21 days ago by
RL
• 0
1
vote
1
reply
136
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago
Layal
• 0
0
votes
2
replies
152
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
22 days ago
michelafrancesconi8
• 0
0
votes
4
replies
229
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by
Michael Love
41k • written 23 days ago by
Aidan
• 0
0
votes
1
reply
142
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 27 days ago by
Michael Love
41k • written 27 days ago by
Mikushi
• 0
2
votes
3
replies
324
views
PCA of different bacterial species
DESeq2
updated 28 days ago by
Michael Love
41k • written 29 days ago by
Laura
▴ 10
1
vote
2
replies
212
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
4 weeks ago • updated 28 days ago
Chanderkant Chaudhary
• 0
0
votes
7
replies
406
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago
fr8712ca-s
• 0
0
votes
7
replies
386
views
DESeq filtering specific to contrasts
DESeq2
updated 5 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
4
replies
565
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 8 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 24 days ago by
Wolfgang Huber
★ 13k • written 9 months ago by
Jane
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 7 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
6
votes
16
replies
2.2k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
695
views
DESeq2 setting significant p-value
DESeq2
updated 5 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 6 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
40 results • Page
1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Awards
• All
Supporter
to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Supporter
to
Jonathan
▴ 10
Popular Question
to
Bine
▴ 40
Locations
• All
United Kingdom,
just now
UPF, Barcelona, Spain,
3 minutes ago
India,
6 minutes ago
Germany,
12 minutes ago
Germany,
15 minutes ago
Traffic: 862 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