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deseq2
•
reset
0
votes
0
replies
10
views
Design formula for circadian time-course data for vst() function
DESeq2
1 hour ago
Vishnu
• 0
1
vote
3
replies
507
views
Filtering after DESeq
DESeq2
IHW
3 days ago • updated 51 minutes ago
caroline.zanchi
• 0
0
votes
1
reply
228
views
Analyzing TnSeq data with DESeq2
DESeq2
updated 5 days ago by
cold.wolverine.arku
• 0 • written 5 days ago by
Lynn
• 0
0
votes
1
reply
632
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 6 days ago by
Michael Love
43k • written 5 weeks ago by
Simran
• 0
0
votes
2
replies
454
views
Differing results with DESeq2
DESeq2
updated 4 days ago by
JKim
• 0 • written 24 days ago by
hampsdiv
• 0
0
votes
2
replies
318
views
RNA Seq using Lrt
DESeq2
7 days ago • updated 5 days ago
Rob
• 0
0
votes
3
replies
719
views
Log2foldchange strange behavior
DESeq2
updated 15 days ago by
ATpoint
★ 4.8k • written 15 days ago by
RambakKulit
• 0
0
votes
1
reply
542
views
WGCNA
WGCNA
DESeq2
updated 17 days ago by
ATpoint
★ 4.8k • written 21 days ago by
bioinformaticssrm2011
• 0
0
votes
1
reply
830
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 17 days ago by
swbarnes2
★ 1.4k • written 18 days ago by
Bioinformatician_R
▴ 20
1
vote
1
reply
1.1k
views
PhD scholar
RNASeqAnalysis
DESeq2
updated 18 days ago by
shepherl
4.1k • written 18 days ago by
Richa
• 0
0
votes
1
reply
289
views
DESeq2 - am I extracting results incorrectly?
DESeq2
updated 20 days ago by
James W. MacDonald
68k • written 21 days ago by
bd2000
▴ 30
1
vote
3
replies
786
views
DESeq - help with pair wise comparisons
DESeq2
22 days ago • updated 21 days ago
bd2000
▴ 30
1
vote
8
replies
2.5k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression
DESeq2
25 days ago • updated 22 days ago
ktz
• 0
0
votes
1
reply
568
views
DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 4 weeks ago by
ATpoint
★ 4.8k • written 4 weeks ago by
Cosmic
• 0
4
votes
6
replies
1.2k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 4 weeks ago by
ATpoint
★ 4.8k • written 7 weeks ago by
Elijah
• 0
1
vote
4
replies
459
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
5 weeks ago
Lennie
• 0
0
votes
4
replies
639
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2
TechnicalReplicates
RNASeq
written 6 weeks ago by
questionanswer
• 0
1
vote
1
reply
807
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2
org.Rn.eg.db
updated 6 weeks ago by
James W. MacDonald
68k • written 6 weeks ago by
Erika
• 0
1
vote
8
replies
2.3k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
6 weeks ago • updated 19 days ago
Luca
• 0
0
votes
2
replies
470
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 6 weeks ago by
Michael Love
43k • written 7 weeks ago by
rohitsatyam102
▴ 20
0
votes
1
reply
233
views
DESeq use in lipidomic analysis
DESeq2
package
Lipidomics
updated 7 weeks ago by
Michael Love
43k • written 7 weeks ago by
泓宇
• 0
0
votes
3
replies
683
views
how many significant figures are there in DESeq2 output
DESeq2
updated 8 weeks ago by
ATpoint
★ 4.8k • written 8 weeks ago by
Matthew McCormack
▴ 180
2
votes
5
replies
1.1k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
8 weeks ago
picasa1983
• 0
3
votes
7
replies
2.1k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 8 weeks ago by
melissa
▴ 10 • written 6.1 years ago by
david.wheeler7
▴ 20
0
votes
1
reply
475
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 8 weeks ago by
James W. MacDonald
68k • written 8 weeks ago by
Sara
• 0
1
vote
1
reply
506
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 9 weeks ago by
swbarnes2
★ 1.4k • written 9 weeks ago by
Len
▴ 10
1
vote
1
reply
322
views
DEseq2 design for additive treatment
DESeq2
updated 9 weeks ago by
ATpoint
★ 4.8k • written 9 weeks ago by
picasa1983
• 0
2
votes
2
replies
617
views
Plot title for PCA in DESeq2
DESeq2
9 weeks ago
AL
• 0
0
votes
3
replies
622
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 9 weeks ago by
Michael Love
43k • written 9 weeks ago by
Marwan
• 0
1
vote
2
replies
1.1k
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 10 weeks ago by
ATpoint
★ 4.8k • written 10 weeks ago by
ingrid.h
• 0
0
votes
1
reply
198
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 11 weeks ago by
Michael Love
43k • written 11 weeks ago by
Sahil
• 0
0
votes
3
replies
580
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 11 weeks ago by
980linnet
• 0 • written 11 weeks ago by
Guilherme
• 0
0
votes
2
replies
431
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 11 weeks ago by
Blair
• 0 • written 12 weeks ago by
A
• 0
0
votes
3
replies
491
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 8 weeks ago by
Leonard
• 0 • written 12 weeks ago by
Martijn
• 0
0
votes
3
replies
512
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 12 weeks ago by
jodan
• 0 • written 3 months ago by
Quang NN
▴ 10
0
votes
1
reply
287
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 12 weeks ago by
Michael Love
43k • written 3 months ago by
Sim
• 0
2
votes
2
replies
514
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 3 months ago by
swbarnes2
★ 1.4k • written 3 months ago by
Nathan
• 0
0
votes
4
replies
1.0k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
3 months ago
Quang NN
▴ 10
0
votes
2
replies
861
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot
DESeq2
3 months ago
Blandine
• 0
0
votes
5
replies
429
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 3 months ago by
georgeyu703
• 0
0
votes
4
replies
675
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
3 months ago
Quang NN
▴ 10
2
votes
5
replies
523
views
Differential variability modelling with vst() expression
limma
DESeq2
written 3 months ago by
jtsy6383
• 0
0
votes
3
replies
661
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 3 months ago by
sindhuri
• 0
2
votes
9
replies
1.2k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
3 months ago
Quang NN
▴ 10
1
vote
1
reply
563
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond
DESeq2
rnaseqDTU
updated 3 months ago by
Michael Love
43k • written 3 months ago by
muhammadsohailraza
• 0
0
votes
1
reply
251
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 3 months ago by
swbarnes2
★ 1.4k • written 3 months ago by
natalievillafranca
• 0
0
votes
1
reply
449
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
updated 3 months ago by
Michael Love
43k • written 4 months ago by
Jimmy Mak
• 0
2
votes
1
reply
458
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 3 months ago by
Michael Love
43k • written 4 months ago by
KR
• 0
0
votes
2
replies
499
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
4 months ago • updated 3 months ago
Kucsera
• 0
1
vote
1
reply
473
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 4 months ago by
Michael Love
43k • written 4 months ago by
txema.heredia
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Filtering after DESeq
by
caroline.zanchi
• 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Comment: Module membership vs gene significance result and Modules-trait relationships re
by
Vinaya
• 0
Hi. I am having the same issue, and haven't found a solution still.
Comment: Feature Counts - potential bug with outfile.jcounts
by
Tom
• 0
[Penistone Locksmith][1] I think that would be a great idea; a novel junction to annotated junction proximity output column. So if the nove…
Comment: Filtering after DESeq
by
caroline.zanchi
• 0
I am going to try this right now, thanks !
Comment: Bioconductor 3.20 Release Schedule
by
randyprice13102000
• 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Votes
Answer: CluserProfiler message "No gene can be mapped"
A: Minfi issue: return code from pthread_create() is 22
Comment: Filtering after DESeq
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
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