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Showing :
DESEq2
•
reset
2
votes
4
replies
1.9k
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 • updated 8 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
789
views
Design formula for circadian time-course data for vst() function
DESeq2
9 months ago
Vishnu
• 0
0
votes
2
replies
948
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
782
views
Differing results with DESeq2
DESeq2
updated 9 months ago by
JKim
• 0 • written 10 months ago by
hampsdiv
• 0
0
votes
2
replies
639
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 9 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 9 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 9 months ago by
Richa
• 0
0
votes
1
reply
526
views
DESeq2 - am I extracting results incorrectly?
DESeq2
updated 9 months ago by
James W. MacDonald
68k • written 9 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
822
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
839
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
10 months ago • updated 9 months ago
Luca
• 0
0
votes
2
replies
839
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 10 months ago by
Michael Love
43k • written 10 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
1.0k
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
1.4k
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
746
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
479
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
927
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
483
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Sahil
• 0
0
votes
3
replies
918
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
968
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 11 months ago by
Blair
• 0 • written 12 months ago by
A
• 0
0
votes
3
replies
654
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
1.1k
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
750
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
774
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
814
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
1.2k
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
983
views
Differential variability modelling with vst() expression
limma
DESeq2
written 12 months ago by
jtsy6383
• 0
0
votes
3
replies
1.1k
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 12 months ago by
sindhuri
• 0
2
votes
9
replies
1.9k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
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
377
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
674
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
789
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: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency)
by
Marina
• 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error
by
ansley.r.burtch
• 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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