Showing : DESeq2 • reset
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DESeq2 from phyloseq error
DESeq2 phyloseq
9 months ago asafpr • 0
3
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1
reply
752
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DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 9 months ago by 68k • written 9 months ago by • 0
1
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5
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1.8k
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Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 9 months ago by 68k • written 9 months ago by ▴ 10
9
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3
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3.4k
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DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 9 months ago by 43k • written 9 months ago by ▴ 40
2
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4
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2.0k
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Filtering after DESeq
DESeq2 IHW
written 10 months ago by ▴ 10
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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
replies
1.9k
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Discrepancies in normalised count data vs unnormalised
DESeq2
10 months ago • updated 9 months ago AMgroup • 0
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2
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821
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Design formula for circadian time-course data for vst() function
DESeq2
10 months ago Vishnu • 0
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2
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984
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Analyzing TnSeq data with DESeq2
DESeq2
written 10 months ago by • 0
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1
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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 10 months ago by 43k • written 11 months ago by • 0
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2
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796
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Differing results with DESeq2
DESeq2
updated 10 months ago by • 0 • written 10 months ago by • 0
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2
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646
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RNA Seq using Lrt
DESeq2
10 months ago Rob • 0
0
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3
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1.1k
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Log2foldchange strange behavior
DESeq2
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
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1
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1.1k
views
WGCNA
WGCNA DESeq2
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
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1
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1.1k
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Comparison of results obtained from a subset of the data versus the complete dataset for a few selected genes.
DESeq2
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 20
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1
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1.4k
views
PhD scholar
RNASeqAnalysis DESeq2
updated 10 months ago by 4.3k • written 10 months ago by • 0
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1
reply
536
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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
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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
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841
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
4
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6
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1.7k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
1
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4
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858
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
11 months ago Lennie • 0
0
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4
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1.7k
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 11 months ago by • 0
1
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2
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1.3k
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
11 months ago • updated 9 months ago Erika • 0
1
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8
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3.0k
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
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2
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872
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 11 months ago by 43k • written 11 months ago by ▴ 20
0
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1
reply
516
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
replies
1.1k
views
how many significant figures are there in DESeq2 output
DESeq2
updated 12 months ago by ★ 5.0k • written 12 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
12 months ago picasa1983 • 0
3
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7
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2.5k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 12 months ago by ▴ 10 • written 7.0 years ago by ▴ 20
0
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1
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1.6k
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 12 months ago by 68k • written 12 months ago by • 0
1
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1
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787
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by ▴ 10
1
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1
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492
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DEseq2 design for additive treatment
DESeq2
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
2
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2
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976
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Plot title for PCA in DESeq2
DESeq2
12 months ago AL • 0
0
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3
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1.2k
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 12 months ago by 43k • written 12 months ago by • 0
1
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2
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1.5k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
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1
reply
514
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 12 months ago by 43k • written 12 months ago by • 0
0
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3
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942
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 12 months ago by • 0 • written 12 months ago by • 0
0
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2
replies
984
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
replies
659
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 12 months ago by • 0 • written 12 months ago by • 0
0
votes
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 13 months ago by ▴ 10
0
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1
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791
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
2
votes
2
replies
814
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
0
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4
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1.5k
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
13 months ago Quang NN ▴ 10
0
votes
2
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1.9k
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
13 months ago Blandine • 0
0
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5
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840
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 13 months ago by • 0
0
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4
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1.4k
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
13 months ago Quang NN ▴ 10
2
votes
5
replies
1.1k
views
Differential variability modelling with vst() expression
limma DESeq2
written 13 months ago by • 0
0
votes
3
replies
1.1k
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 13 months ago by • 0
2
votes
9
replies
2.1k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
13 months ago Quang NN ▴ 10
4,851 results • Page 2 of 98
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Replies
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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