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DESEQ2
•
reset
0
votes
0
replies
9
views
What Input-type do I use in decouplR::run_viper?
decoupleR
viper
DESeq2
2 hours ago
Julian
• 0
0
votes
1
reply
58
views
DESeq2 from phyloseq error
DESeq2
phyloseq
9 hours ago • updated 4 hours ago
asafpr
• 0
0
votes
0
replies
83
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
5 days ago
dudutchy
• 0
3
votes
1
reply
334
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2
apeglm
updated 6 days ago by
James W. MacDonald
68k • written 6 days ago by
sk
• 0
1
vote
5
replies
977
views
Heatmap of a transformed deseq object with pheatmap
DESeq2
heatmaps
updated 6 days ago by
James W. MacDonald
68k • written 6 days ago by
caroline.zanchi
▴ 10
0
votes
0
replies
62
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
7 days ago
s.malik
• 0
8
votes
3
replies
2.5k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 11 days ago by
Michael Love
43k • written 13 days ago by
Cassia
▴ 40
2
votes
3
replies
1.3k
views
Filtering after DESeq
DESeq2
IHW
updated 14 days ago by
ChaseWendrix
• 0 • written 24 days ago by
caroline.zanchi
▴ 10
0
votes
4
replies
951
views
DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
15 days ago • updated 9 days ago
sk
• 0
4
votes
6
replies
1.6k
views
parameters of filterByExpr
edgeR
DESeq2
filterByExpr
updated 3 days ago by
Paul Harrison
▴ 110 • written 16 days ago by
caroline.zanchi
▴ 10
0
votes
4
replies
677
views
Discrepancies in normalised count data vs unnormalised
DESeq2
19 days ago • updated 4 hours ago
AMgroup
• 0
0
votes
2
replies
487
views
Design formula for circadian time-course data for vst() function
DESeq2
20 days ago • updated 19 days ago
Vishnu
• 0
0
votes
2
replies
611
views
Analyzing TnSeq data with DESeq2
DESeq2
written 25 days ago by
newfunland
• 0
0
votes
1
reply
962
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 27 days ago by
Michael Love
43k • written 7 weeks ago by
Simran
• 0
0
votes
2
replies
514
views
Differing results with DESeq2
DESeq2
updated 25 days ago by
JKim
• 0 • written 6 weeks ago by
hampsdiv
• 0
0
votes
2
replies
384
views
RNA Seq using Lrt
DESeq2
27 days ago • updated 26 days ago
Rob
• 0
0
votes
3
replies
781
views
Log2foldchange strange behavior
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.8k • written 5 weeks ago by
RambakKulit
• 0
0
votes
1
reply
620
views
WGCNA
WGCNA
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.8k • written 5 weeks ago by
bioinformaticssrm2011
• 0
0
votes
1
reply
884
views
Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 5 weeks ago by
swbarnes2
★ 1.4k • written 5 weeks ago by
Bioinformatician_R
▴ 20
1
vote
1
reply
1.2k
views
PhD scholar
RNASeqAnalysis
DESeq2
updated 5 weeks ago by
shepherl
4.1k • written 5 weeks ago by
Richa
• 0
0
votes
1
reply
342
views
DESeq2 - am I extracting results incorrectly?
DESeq2
updated 5 weeks ago by
James W. MacDonald
68k • written 5 weeks ago by
bd2000
▴ 30
1
vote
3
replies
817
views
DESeq - help with pair wise comparisons
DESeq2
6 weeks ago
bd2000
▴ 30
1
vote
8
replies
2.6k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression
DESeq2
6 weeks ago
ktz
• 0
0
votes
1
reply
589
views
DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 7 weeks ago by
ATpoint
★ 4.8k • written 7 weeks ago by
Cosmic
• 0
4
votes
6
replies
1.3k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 7 weeks ago by
ATpoint
★ 4.8k • written 10 weeks ago by
Elijah
• 0
1
vote
4
replies
517
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
8 weeks ago • updated 7 weeks ago
Lennie
• 0
0
votes
4
replies
772
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2
TechnicalReplicates
RNASeq
written 8 weeks ago by
questionanswer
• 0
1
vote
1
reply
837
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2
org.Rn.eg.db
updated 9 weeks ago by
James W. MacDonald
68k • written 9 weeks ago by
Erika
• 0
1
vote
8
replies
2.4k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
9 weeks ago • updated 5 weeks ago
Luca
• 0
0
votes
2
replies
507
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 9 weeks ago by
Michael Love
43k • written 10 weeks ago by
rohitsatyam102
▴ 20
0
votes
1
reply
253
views
DESeq use in lipidomic analysis
DESeq2
package
Lipidomics
updated 10 weeks ago by
Michael Love
43k • written 10 weeks ago by
泓宇
• 0
0
votes
3
replies
709
views
how many significant figures are there in DESeq2 output
DESeq2
updated 11 weeks ago by
ATpoint
★ 4.8k • written 11 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
11 weeks ago
picasa1983
• 0
3
votes
7
replies
2.1k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 11 weeks ago by
melissa
▴ 10 • written 6.2 years ago by
david.wheeler7
▴ 20
0
votes
1
reply
611
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 weeks ago by
James W. MacDonald
68k • written 11 weeks ago by
Sara
• 0
1
vote
1
reply
527
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 11 weeks ago by
swbarnes2
★ 1.4k • written 12 weeks ago by
Len
▴ 10
1
vote
1
reply
344
views
DEseq2 design for additive treatment
DESeq2
updated 12 weeks ago by
ATpoint
★ 4.8k • written 12 weeks ago by
picasa1983
• 0
2
votes
2
replies
667
views
Plot title for PCA in DESeq2
DESeq2
12 weeks ago • updated 11 weeks ago
AL
• 0
0
votes
3
replies
659
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 12 weeks ago by
Michael Love
43k • written 12 weeks ago by
Marwan
• 0
1
vote
2
replies
1.1k
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 3 months ago by
ATpoint
★ 4.8k • written 3 months ago by
ingrid.h
• 0
0
votes
1
reply
225
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Sahil
• 0
0
votes
3
replies
611
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 3 months ago by
980linnet
• 0 • written 3 months ago by
Guilherme
• 0
0
votes
2
replies
458
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 3 months ago by
Blair
• 0 • written 3 months ago by
A
• 0
0
votes
3
replies
515
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 11 weeks ago by
Leonard
• 0 • written 3 months ago by
Martijn
• 0
0
votes
3
replies
566
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 3 months ago by
jodan
• 0 • written 3 months ago by
Quang NN
▴ 10
0
votes
1
reply
322
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Sim
• 0
2
votes
2
replies
537
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
1.1k
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
1.0k
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
455
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
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Comment: Can't install BioC packages (and manager) behind firewall
by
Marcel Ramos
700
Hi Delphine, Please make sure that your SSL certificates are up to date. Check with your system's administrator. Your browser may be usin…
Comment: Limma trend with limpa
by
Alejandro
• 0
Dear Gordon, Thank you very much!
Answer: DESeq2 from phyloseq error
by
asafpr
• 0
Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …
Comment: Discrepancies in normalised count data vs unnormalised
by
AMgroup
• 0
Thank you for your reply! There are some pretty big discrepancies in the total raw counts between samples: ![enter image description here…
Answer: Limma trend with limpa
by
Gordon Smyth
52k
Dear Alejandro, Thanks for your interest. No, one does not set `trend=TRUE` when running eBayes() after dpcDE(). The variance trends are …
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Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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