Showing : Deseq2 • reset
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 1 day ago by 43k • written 2 days ago by • 0
2
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2
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348
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 2 days ago by ★ 1.4k • written 6 days ago by • 0
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4
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852
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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
5 days ago • updated 2 days ago Quang NN ▴ 10
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2
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200
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
5 days ago • updated 2 days ago Quang NN ▴ 10
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2
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250
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
8 days ago • updated 6 days ago Blandine • 0
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4
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206
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
8 days ago georgeyu703 • 0
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4
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379
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
10 days ago • updated 8 days ago Quang NN ▴ 10
2
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5
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319
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Differential variability modelling with vst() expression
limma DESeq2
written 21 days ago by • 0
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2
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375
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
21 days ago • updated 19 days ago sindhuri • 0
2
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9
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787
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
22 days ago • updated 10 days ago Quang NN ▴ 10
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1
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302
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 23 days ago by 43k • written 23 days ago by • 0
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1
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179
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 24 days ago by ★ 1.4k • written 24 days ago by • 0
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1
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358
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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 26 days ago by 43k • written 5 weeks ago by • 0
2
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1
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354
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 26 days ago by 43k • written 4 weeks ago by • 0
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2
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289
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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 5 weeks ago by 43k • written 7 weeks ago by • 0
1
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9
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838
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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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327
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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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571
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Deseq2 Design
RNASeq DESeq2
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
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5
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520
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p value is 0, padj is 0
DESeq2
7 weeks ago • updated 6 weeks ago Wirayatida • 0
1
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2
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516
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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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826
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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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289
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by ▴ 20
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3
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430
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DESeq2 - Comparing Comparisons
DESeq2
updated 7 weeks ago by 67k • written 8 weeks ago by • 0
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4
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562
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lfcShrink and alpha value
lfcShrink DESeq2
8 weeks ago cropero • 0
2
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1
reply
313
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
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2
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234
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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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275
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
9 weeks ago Anna • 0
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2
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566
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Deseq2 res Function
DESeq2
updated 9 weeks ago by 67k • written 9 weeks ago by ▴ 10
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4
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455
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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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474
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Identical samples after deseq2 batch effect removal
DESeq2
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
0
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1
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268
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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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322
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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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178
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eRNAs count
RNASeq DESeq2
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
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417
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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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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
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1
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251
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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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654
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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 4 days ago by • 0 • written 6.1 years ago by ▴ 30
1
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6
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1.0k
views
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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402
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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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713
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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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431
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Average expression of genes across replicates
DESeq2
updated 12 weeks ago by ★ 4.6k • written 3 months ago by • 0
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164
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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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377
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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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895
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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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962
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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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388
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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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341
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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: 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!
Comment: build samplesheet and plot profile by yf • 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Votes
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
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