Showing : deseq2 • reset
2
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2.0k
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Filtering after DESeq
DESeq2 IHW
written 9 months ago by ▴ 10
0
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4
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1.3k
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DESEQ2 - Correctly altering log2foldchange when switching comparison direction (HELP GREATLY APPRECIATED)
DESeq2
9 months ago sk • 0
0
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6
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1.9k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
9 months ago • updated 8 months ago AMgroup • 0
0
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2
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792
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Design formula for circadian time-course data for vst() function
DESeq2
9 months ago Vishnu • 0
0
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2
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951
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Analyzing TnSeq data with DESeq2
DESeq2
written 9 months ago by • 0
0
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1
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1.3k
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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 43k • written 10 months ago by • 0
0
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2
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784
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Differing results with DESeq2
DESeq2
updated 9 months ago by • 0 • written 10 months ago by • 0
0
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2
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642
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RNA Seq using Lrt
DESeq2
9 months ago Rob • 0
0
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3
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1.1k
views
Log2foldchange strange behavior
DESeq2
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
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1
reply
1.0k
views
WGCNA
WGCNA DESeq2
updated 9 months ago by ★ 5.0k • written 10 months ago by • 0
0
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1
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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 ★ 1.4k • written 10 months ago by ▴ 20
1
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1
reply
1.4k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 9 months ago by 4.3k • written 10 months ago by • 0
0
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1
reply
529
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DESeq2 - am I extracting results incorrectly?
DESeq2
updated 10 months ago by 68k • written 10 months ago by ▴ 30
1
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3
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1.1k
views
DESeq - help with pair wise comparisons
DESeq2
10 months ago bd2000 ▴ 30
1
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8
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3.1k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
10 months ago ktz • 0
0
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1
reply
825
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
4
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6
replies
1.7k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 10 months ago by ★ 5.0k • written 11 months ago by • 0
1
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4
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845
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
10 months ago Lennie • 0
0
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4
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1.5k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 10 months ago by • 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
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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
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844
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 10 months ago by 43k • written 11 months ago by ▴ 20
0
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1
reply
501
views
DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 11 months ago by 43k • written 11 months ago by • 0
0
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3
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1.1k
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how many significant figures are there in DESeq2 output
DESeq2
updated 11 months ago by ★ 5.0k • written 11 months ago by ▴ 180
2
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5
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1.5k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
11 months ago picasa1983 • 0
3
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7
replies
2.5k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 11 months ago by ▴ 10 • written 6.9 years ago by ▴ 20
0
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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 68k • written 11 months ago by • 0
1
vote
1
reply
748
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 10
1
vote
1
reply
480
views
DEseq2 design for additive treatment
DESeq2
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
2
votes
2
replies
944
views
Plot title for PCA in DESeq2
DESeq2
11 months ago AL • 0
0
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3
replies
1.2k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
1
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2
replies
1.4k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 11 months ago by ★ 5.0k • written 11 months ago by • 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 43k • written 12 months ago by • 0
0
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3
replies
922
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 11 months ago by • 0 • written 12 months ago by • 0
0
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2
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970
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 12 months ago by • 0 • written 12 months ago by • 0
0
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3
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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 • 0 • written 12 months ago by • 0
0
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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 • 0 • written 12 months ago by ▴ 10
0
votes
1
reply
752
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
2
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2
replies
777
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
0
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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
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2
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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
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5
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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 • 0
0
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4
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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 • 0
0
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3
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1.1k
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 13 months ago by • 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 43k • written 13 months ago by • 0
0
votes
1
reply
379
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 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 43k • written 13 months ago by • 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 43k • written 13 months ago by • 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
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