Showing : DESEq2 • reset
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 3 days ago by 43k • written 4 days ago by • 0
2
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2
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373
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 4 days ago by ★ 1.4k • written 8 days ago by • 0
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4
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875
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Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
6 days ago • updated 4 days ago Quang NN ▴ 10
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2
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211
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
6 days ago • updated 4 days ago Quang NN ▴ 10
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2
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257
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
10 days ago • updated 8 days ago Blandine • 0
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4
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215
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
10 days ago georgeyu703 • 0
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4
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384
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
12 days ago • updated 10 days ago Quang NN ▴ 10
2
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5
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321
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Differential variability modelling with vst() expression
limma DESeq2
written 23 days ago by • 0
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2
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376
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
23 days ago • updated 21 days ago sindhuri • 0
2
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9
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795
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
24 days ago • updated 12 days ago Quang NN ▴ 10
1
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1
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309
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 25 days ago by 43k • written 25 days ago by • 0
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1
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182
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 26 days ago by ★ 1.4k • written 26 days ago by • 0
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1
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360
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 28 days ago by 43k • written 5 weeks ago by • 0
2
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1
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358
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 28 days ago by 43k • written 5 weeks ago by • 0
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2
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291
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
4 weeks ago Kucsera • 0
1
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1
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377
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
1
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9
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846
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 6 weeks ago by ▴ 30
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2
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330
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 6 weeks ago by ★ 4.6k • written 7 weeks ago by • 0
1
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5
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576
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Deseq2 Design
RNASeq DESeq2
updated 6 weeks ago by 67k • written 7 weeks ago by • 0
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5
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524
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p value is 0, padj is 0
DESeq2
7 weeks ago Wirayatida • 0
1
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2
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518
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
7 weeks ago georgii.vdovin • 0
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7
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830
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 7 weeks ago by • 0 • written 7 weeks ago by • 0
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1
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291
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by ▴ 20
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3
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433
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DESeq2 - Comparing Comparisons
DESeq2
updated 7 weeks ago by 67k • written 8 weeks ago by • 0
0
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4
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564
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lfcShrink and alpha value
lfcShrink DESeq2
9 weeks ago • updated 8 weeks ago cropero • 0
2
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1
reply
314
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
0
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2
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237
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
0
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2
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276
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
9 weeks ago Anna • 0
1
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2
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567
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Deseq2 res Function
DESeq2
updated 9 weeks ago by 67k • written 10 weeks ago by ▴ 10
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4
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458
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
10 weeks ago NB • 0
0
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5
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478
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Identical samples after deseq2 batch effect removal
DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
0
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1
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271
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 10 weeks ago by 67k • written 10 weeks ago by • 0
1
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2
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325
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
10 weeks ago Denise • 0
0
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1
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179
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eRNAs count
RNASeq DESeq2
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
0
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1
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421
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DESeq2 rerun returns different results
DESeq2
updated 11 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
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1
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274
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 11 weeks ago by 43k • written 11 weeks ago by • 0
0
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1
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254
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
2
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2
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655
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Handling biological replicates in DESeq2
DESeq2
updated 11 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
5
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2
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26k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 6 days ago by • 0 • written 6.1 years ago by ▴ 30
1
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6
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1.1k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 10
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2
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408
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 12 weeks ago by • 0
4
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5
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715
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
12 weeks ago LuciaNhu • 0
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1
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435
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Average expression of genes across replicates
DESeq2
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
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0
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166
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
3 months ago info ▴ 10
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10
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1.4k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
3 months ago • updated 12 weeks ago Denise • 0
0
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1
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378
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Deseq to output continous sequencing data
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
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4
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899
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Adjusted p-values become NA when sub-setting samples
DESeq2
3 months ago • updated 12 weeks ago txema.heredia • 0
3
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3
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966
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 3 months ago by • 0
0
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2
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389
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 3 months ago by • 0
0
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1
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342
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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