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
2
votes
4
replies
2.0k
views
Filtering after DESeq
DESeq2
IHW
written 9 months ago by
caroline.zanchi
▴ 10
0
votes
4
replies
1.3k
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
9 months ago
sk
• 0
0
votes
6
replies
1.9k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
9 months ago • updated 8 months ago
AMgroup
• 0
0
votes
2
replies
792
views
Design formula for circadian time-course data for vst() function
DESeq2
9 months ago
Vishnu
• 0
0
votes
2
replies
951
views
Analyzing TnSeq data with DESeq2
DESeq2
written 9 months ago by
newfunland
• 0
0
votes
1
reply
1.3k
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 9 months ago by
Michael Love
43k • written 10 months ago by
Simran
• 0
0
votes
2
replies
784
views
Differing results with DESeq2
DESeq2
updated 9 months ago by
JKim
• 0 • written 10 months ago by
hampsdiv
• 0
0
votes
2
replies
642
views
RNA Seq using Lrt
DESeq2
9 months ago
Rob
• 0
0
votes
3
replies
1.1k
views
Log2foldchange strange behavior
DESeq2
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
RambakKulit
• 0
0
votes
1
reply
1.0k
views
WGCNA
WGCNA
DESeq2
updated 9 months ago by
ATpoint
★ 5.0k • written 10 months ago by
bioinformaticssrm2011
• 0
0
votes
1
reply
1.1k
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 9 months ago by
swbarnes2
★ 1.4k • written 10 months ago by
Bioinformatician_R
▴ 20
1
vote
1
reply
1.4k
views
PhD scholar
RNASeqAnalysis
DESeq2
updated 9 months ago by
shepherl
4.3k • written 10 months ago by
Richa
• 0
0
votes
1
reply
529
views
DESeq2 - am I extracting results incorrectly?
DESeq2
updated 10 months ago by
James W. MacDonald
68k • written 10 months ago by
bd2000
▴ 30
1
vote
3
replies
1.1k
views
DESeq - help with pair wise comparisons
DESeq2
10 months ago
bd2000
▴ 30
1
vote
8
replies
3.1k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression
DESeq2
10 months ago
ktz
• 0
0
votes
1
reply
825
views
DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
Cosmic
• 0
4
votes
6
replies
1.7k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 10 months ago by
ATpoint
★ 5.0k • written 11 months ago by
Elijah
• 0
1
vote
4
replies
845
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
10 months ago
Lennie
• 0
0
votes
4
replies
1.5k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2
TechnicalReplicates
RNASeq
written 10 months ago by
questionanswer
• 0
1
vote
2
replies
1.3k
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2
org.Rn.eg.db
10 months ago • updated 8 months ago
Erika
• 0
1
vote
8
replies
2.9k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
11 months ago • updated 10 months ago
Luca
• 0
0
votes
2
replies
844
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 10 months ago by
Michael Love
43k • written 11 months ago by
rohitsatyam102
▴ 20
0
votes
1
reply
501
views
DESeq use in lipidomic analysis
DESeq2
package
Lipidomics
updated 11 months ago by
Michael Love
43k • written 11 months ago by
泓宇
• 0
0
votes
3
replies
1.1k
views
how many significant figures are there in DESeq2 output
DESeq2
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
Matthew McCormack
▴ 180
2
votes
5
replies
1.5k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
11 months ago
picasa1983
• 0
3
votes
7
replies
2.5k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 11 months ago by
melissa
▴ 10 • written 6.9 years ago by
david.wheeler7
▴ 20
0
votes
1
reply
1.5k
views
How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData
DESeq2
pseudobulk
sing
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Sara
• 0
1
vote
1
reply
748
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 11 months ago by
swbarnes2
★ 1.4k • written 11 months ago by
Len
▴ 10
1
vote
1
reply
480
views
DEseq2 design for additive treatment
DESeq2
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
picasa1983
• 0
2
votes
2
replies
944
views
Plot title for PCA in DESeq2
DESeq2
11 months ago
AL
• 0
0
votes
3
replies
1.2k
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Marwan
• 0
1
vote
2
replies
1.4k
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
ingrid.h
• 0
0
votes
1
reply
487
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 11 months ago by
Michael Love
43k • written 12 months ago by
Sahil
• 0
0
votes
3
replies
922
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 11 months ago by
980linnet
• 0 • written 12 months ago by
Guilherme
• 0
0
votes
2
replies
970
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 12 months ago by
Blair
• 0 • written 12 months ago by
A
• 0
0
votes
3
replies
655
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 11 months ago by
Leonard
• 0 • written 12 months ago by
Martijn
• 0
0
votes
3
replies
1.2k
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 12 months ago by
jodan
• 0 • written 12 months ago by
Quang NN
▴ 10
0
votes
1
reply
752
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 12 months ago by
Michael Love
43k • written 12 months ago by
Sim
• 0
2
votes
2
replies
777
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 12 months ago by
swbarnes2
★ 1.4k • written 12 months ago by
Nathan
• 0
0
votes
4
replies
1.5k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
12 months ago
Quang NN
▴ 10
0
votes
2
replies
1.7k
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot
DESeq2
12 months ago
Blandine
• 0
0
votes
5
replies
817
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 12 months ago by
georgeyu703
• 0
0
votes
4
replies
1.3k
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
12 months ago
Quang NN
▴ 10
2
votes
5
replies
988
views
Differential variability modelling with vst() expression
limma
DESeq2
written 13 months ago by
jtsy6383
• 0
0
votes
3
replies
1.1k
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 13 months ago by
sindhuri
• 0
2
votes
9
replies
2.0k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
13 months ago • updated 12 months ago
Quang NN
▴ 10
1
vote
1
reply
1.3k
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond
DESeq2
rnaseqDTU
updated 13 months ago by
Michael Love
43k • written 13 months ago by
muhammadsohailraza
• 0
0
votes
1
reply
379
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 13 months ago by
swbarnes2
★ 1.4k • written 13 months ago by
natalievillafranca
• 0
0
votes
1
reply
678
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
Jimmy Mak
• 0
2
votes
1
reply
790
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 13 months ago by
Michael Love
43k • written 13 months ago by
KR
• 0
4,848 results • Page
2 of 97
Recent ...
Replies
Comment: using limma trend workflow in CAMERA
by
Gordon Smyth
53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results
by
Tikaaa2sahaaaq2c
• 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA
by
A.Barden
▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Tikaaa2sahaaaq2c
• 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase
by
DamionLedner99
• 0
thanks for sharing!!! https://cran.r-project.org/
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
Awards
• All
Teacher
to
Michael Love
43k
Supporter
to
fl
▴ 20
Popular Question
to
James W. MacDonald
68k
Popular Question
to
rcavalca
▴ 140
Popular Question
to
James Aiden
• 0
Locations
• All
United States,
21 minutes ago
Germany,
26 minutes ago
United States,
41 minutes ago
The city by the bay,
1 hour ago
WEHI, Melbourne, Australia,
1 hour ago
Traffic: 1334 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