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DESeq2
•
reset
0
votes
2
replies
605
views
RNA Seq using Lrt
DESeq2
7 months ago
Rob
• 0
0
votes
3
replies
1.0k
views
Log2foldchange strange behavior
DESeq2
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
RambakKulit
• 0
0
votes
1
reply
913
views
WGCNA
WGCNA
DESeq2
updated 8 months ago by
ATpoint
★ 5.0k • written 8 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 8 months ago by
swbarnes2
★ 1.4k • written 8 months ago by
Bioinformatician_R
▴ 20
1
vote
1
reply
1.3k
views
PhD scholar
RNASeqAnalysis
DESeq2
updated 8 months ago by
shepherl
4.2k • written 8 months ago by
Richa
• 0
0
votes
1
reply
493
views
DESeq2 - am I extracting results incorrectly?
DESeq2
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
bd2000
▴ 30
1
vote
3
replies
1.1k
views
DESeq - help with pair wise comparisons
DESeq2
8 months ago
bd2000
▴ 30
1
vote
8
replies
3.0k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression
DESeq2
8 months ago
ktz
• 0
0
votes
1
reply
771
views
DESeq2
org.Mmu.eg.db
DESeq2
TimeCourse
DMSOvsdrug
RNASeqData
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
Cosmic
• 0
4
votes
6
replies
1.6k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2
DEXSeq
updated 8 months ago by
ATpoint
★ 5.0k • written 9 months ago by
Elijah
• 0
1
vote
4
replies
760
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
8 months ago
Lennie
• 0
0
votes
4
replies
1.2k
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2
TechnicalReplicates
RNASeq
written 8 months ago by
questionanswer
• 0
1
vote
2
replies
1.2k
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2
org.Rn.eg.db
9 months ago • updated 6 months ago
Erika
• 0
1
vote
8
replies
2.7k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
9 months ago • updated 8 months ago
Luca
• 0
0
votes
2
replies
747
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 8 months ago by
Michael Love
43k • written 9 months ago by
rohitsatyam102
▴ 20
0
votes
1
reply
465
views
DESeq use in lipidomic analysis
DESeq2
package
Lipidomics
updated 9 months ago by
Michael Love
43k • written 9 months ago by
泓宇
• 0
0
votes
3
replies
993
views
how many significant figures are there in DESeq2 output
DESeq2
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
Matthew McCormack
▴ 180
2
votes
5
replies
1.4k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
9 months ago
picasa1983
• 0
3
votes
7
replies
2.4k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 9 months ago by
melissa
▴ 10 • written 6.8 years ago by
david.wheeler7
▴ 20
0
votes
1
reply
882
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 9 months ago by
James W. MacDonald
68k • written 9 months ago by
Sara
• 0
1
vote
1
reply
657
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 9 months ago by
swbarnes2
★ 1.4k • written 9 months ago by
Len
▴ 10
1
vote
1
reply
453
views
DEseq2 design for additive treatment
DESeq2
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
picasa1983
• 0
2
votes
2
replies
828
views
Plot title for PCA in DESeq2
DESeq2
9 months ago
AL
• 0
0
votes
3
replies
1.0k
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 9 months ago by
Michael Love
43k • written 9 months ago by
Marwan
• 0
1
vote
2
replies
1.4k
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
ingrid.h
• 0
0
votes
1
reply
415
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 10 months ago by
Michael Love
43k • written 10 months ago by
Sahil
• 0
0
votes
3
replies
832
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 10 months ago by
980linnet
• 0 • written 10 months ago by
Guilherme
• 0
0
votes
2
replies
923
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 10 months ago by
Blair
• 0 • written 10 months ago by
A
• 0
0
votes
3
replies
615
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 9 months ago by
Leonard
• 0 • written 10 months ago by
Martijn
• 0
0
votes
3
replies
876
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 10 months ago by
jodan
• 0 • written 10 months ago by
Quang NN
▴ 10
0
votes
1
reply
660
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 10 months ago by
Michael Love
43k • written 10 months ago by
Sim
• 0
2
votes
2
replies
702
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 10 months ago by
swbarnes2
★ 1.4k • written 10 months ago by
Nathan
• 0
0
votes
4
replies
1.4k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
10 months ago
Quang NN
▴ 10
0
votes
2
replies
1.3k
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot
DESeq2
10 months ago
Blandine
• 0
0
votes
5
replies
727
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 10 months ago by
georgeyu703
• 0
0
votes
4
replies
968
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
10 months ago
Quang NN
▴ 10
2
votes
5
replies
816
views
Differential variability modelling with vst() expression
limma
DESeq2
written 11 months ago by
jtsy6383
• 0
0
votes
3
replies
924
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 11 months ago by
sindhuri
• 0
2
votes
9
replies
1.7k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
11 months ago • updated 10 months ago
Quang NN
▴ 10
1
vote
1
reply
900
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond
DESeq2
rnaseqDTU
updated 11 months ago by
Michael Love
43k • written 11 months ago by
muhammadsohailraza
• 0
0
votes
1
reply
341
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 11 months ago by
swbarnes2
★ 1.4k • written 11 months ago by
natalievillafranca
• 0
0
votes
1
reply
606
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Jimmy Mak
• 0
2
votes
1
reply
731
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 11 months ago by
Michael Love
43k • written 11 months ago by
KR
• 0
0
votes
2
replies
717
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
11 months ago
Kucsera
• 0
1
vote
1
reply
553
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 11 months ago by
Michael Love
43k • written 12 months ago by
txema.heredia
• 0
1
vote
9
replies
1.5k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 11 months ago by
anna.cot.anna.cot
▴ 40
4
votes
2
replies
1.0k
views
Standardization of rlog transformed counts before PCA
RNASeq
DESeq2
Visualization
updated 11 months ago by
ATpoint
★ 5.0k • written 12 months ago by
bbao
▴ 10
1
vote
5
replies
1.0k
views
Deseq2 Design
RNASeq
DESeq2
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
pm_25
• 0
0
votes
5
replies
1.2k
views
p value is 0, padj is 0
DESeq2
12 months ago
Wirayatida
• 0
1
vote
2
replies
1.1k
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
12 months ago
georgii.vdovin
• 0
4,841 results • Page
2 of 97
Recent ...
Replies
Comment: p.adjust BH Question
by
TikTsoksocissalpc
• 0
Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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