Showing : DEseq2 • reset
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 10 hours ago by 67k • written 16 hours ago by • 0
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2
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195
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
2 days ago • updated 12 hours ago Blandine • 0
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4
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175
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
3 days ago georgeyu703 • 0
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4
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354
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
4 days ago • updated 2 days ago Quang NN ▴ 10
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5
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294
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Differential variability modelling with vst() expression
limma DESeq2
written 15 days ago by • 0
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2
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360
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
16 days ago • updated 13 days ago sindhuri • 0
2
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9
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735
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
16 days ago • updated 4 days ago Quang NN ▴ 10
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288
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 17 days ago by 43k • written 17 days ago by • 0
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1
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162
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 18 days ago by ★ 1.4k • written 18 days ago by • 0
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1
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349
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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 21 days ago by 43k • written 4 weeks ago by • 0
2
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1
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345
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 21 days ago by 43k • written 28 days ago by • 0
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2
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265
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
27 days ago • updated 25 days ago Kucsera • 0
1
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1
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368
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 5 weeks ago by 43k • written 6 weeks ago by • 0
1
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9
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815
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 5 weeks ago by ▴ 30
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2
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316
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 5 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
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5
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561
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Deseq2 Design
RNASeq DESeq2
updated 5 weeks ago by 67k • written 6 weeks ago by • 0
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5
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509
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p value is 0, padj is 0
DESeq2
6 weeks ago Wirayatida • 0
1
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2
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493
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
6 weeks ago georgii.vdovin • 0
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7
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804
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 6 weeks ago by • 0 • written 6 weeks ago by • 0
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1
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283
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 6 weeks ago by 43k • written 7 weeks ago by ▴ 20
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3
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422
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DESeq2 - Comparing Comparisons
DESeq2
updated 6 weeks ago by 67k • written 7 weeks ago by • 0
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4
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546
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lfcShrink and alpha value
lfcShrink DESeq2
8 weeks ago • updated 7 weeks ago cropero • 0
2
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1
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299
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 7 weeks ago by 43k • written 8 weeks ago by • 0
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2
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223
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
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2
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267
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
8 weeks ago Anna • 0
1
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2
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559
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Deseq2 res Function
DESeq2
updated 8 weeks ago by 67k • written 8 weeks ago by ▴ 10
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4
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448
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
9 weeks ago NB • 0
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5
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457
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Identical samples after deseq2 batch effect removal
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
0
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1
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257
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 9 weeks ago by 67k • written 9 weeks ago by • 0
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2
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316
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
9 weeks ago Denise • 0
0
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1
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171
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eRNAs count
RNASeq DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
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1
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409
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DESeq2 rerun returns different results
DESeq2
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
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1
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264
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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247
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 10 weeks ago by ★ 4.1k • written 10 weeks ago by • 0
2
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2
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648
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Handling biological replicates in DESeq2
DESeq2
updated 10 weeks ago by ★ 4.6k • written 10 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
written 6.0 years ago by ▴ 30
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6
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1.0k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 11 weeks ago by 43k • written 11 weeks ago by ▴ 10
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2
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396
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 11 weeks ago by • 0
4
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5
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697
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
11 weeks ago LuciaNhu • 0
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1
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422
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Average expression of genes across replicates
DESeq2
updated 11 weeks ago by ★ 4.6k • written 12 weeks ago by • 0
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161
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
12 weeks 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
12 weeks ago • updated 11 weeks ago Denise • 0
0
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1
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371
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Deseq to output continous sequencing data
DESeq2
updated 12 weeks ago by 43k • written 3 months ago by • 0
1
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4
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877
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Adjusted p-values become NA when sub-setting samples
DESeq2
3 months ago • updated 11 weeks ago txema.heredia • 0
3
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3
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951
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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
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2
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383
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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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334
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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
2
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3
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1.1k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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4
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814
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DESeq2 - interactions when using factors concatenated into group
DESeq2
3 months ago boczniak767 ▴ 740
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235
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
3 months ago JY • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…
Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k
Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…
Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0
Thank you so much ! It's working !
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k
Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…
Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k
Thanks @fep29! ^^
Votes
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
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