Showing : DeSeq2 • reset
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 1 day ago by ★ 4.7k • written 2 days ago by • 0
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1
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112
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 5 days ago by 43k • written 9 days ago by • 0
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3
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413
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 5 days ago by • 0 • written 10 days ago by • 0
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2
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321
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 8 days ago by • 0 • written 13 days ago by • 0
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2
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292
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
13 days ago • updated 12 days ago Martijn • 0
0
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3
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329
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 13 days ago by • 0 • written 21 days ago by ▴ 10
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1
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133
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 18 days ago by 43k • written 19 days ago by • 0
2
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2
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413
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 19 days ago by ★ 1.4k • written 23 days ago by • 0
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4
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916
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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
21 days ago • updated 19 days ago Quang NN ▴ 10
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2
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329
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
25 days ago • updated 23 days ago Blandine • 0
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5
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293
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 25 days ago by • 0
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4
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427
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
27 days ago • updated 25 days ago Quang NN ▴ 10
2
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5
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354
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Differential variability modelling with vst() expression
limma DESeq2
written 5 weeks ago by • 0
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3
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509
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 5 weeks ago by • 0
2
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9
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869
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
5 weeks ago • updated 27 days ago Quang NN ▴ 10
1
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1
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345
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
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1
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193
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 5 weeks ago by ★ 1.4k • written 5 weeks ago by • 0
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1
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375
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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 6 weeks ago by 43k • written 7 weeks ago by • 0
2
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1
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369
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
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2
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323
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
7 weeks ago • updated 6 weeks ago Kucsera • 0
1
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1
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387
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
1
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9
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864
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 8 weeks ago by ▴ 30
4
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2
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431
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 8 weeks ago by ★ 4.7k • written 9 weeks ago by ▴ 10
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5
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605
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Deseq2 Design
RNASeq DESeq2
updated 8 weeks ago by 68k • written 9 weeks ago by • 0
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5
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567
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p value is 0, padj is 0
DESeq2
9 weeks ago Wirayatida • 0
1
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2
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548
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
9 weeks ago georgii.vdovin • 0
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7
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875
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 9 weeks ago by • 0 • written 9 weeks ago by • 0
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1
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310
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by ▴ 20
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3
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449
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DESeq2 - Comparing Comparisons
DESeq2
updated 9 weeks ago by 68k • written 10 weeks ago by • 0
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4
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581
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lfcShrink and alpha value
lfcShrink DESeq2
11 weeks ago • updated 10 weeks ago cropero • 0
2
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1
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340
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 10 weeks ago by 43k • written 11 weeks ago by • 0
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246
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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2
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288
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
11 weeks ago Anna • 0
1
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2
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581
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Deseq2 res Function
DESeq2
updated 11 weeks ago by 68k • written 12 weeks ago by ▴ 10
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4
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476
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
12 weeks ago NB • 0
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5
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498
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Identical samples after deseq2 batch effect removal
DESeq2
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
0
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1
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283
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
1
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2
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344
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
12 weeks ago Denise • 0
0
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1
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194
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eRNAs count
RNASeq DESeq2
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
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1
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440
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DESeq2 rerun returns different results
DESeq2
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
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1
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294
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 3 months ago by 43k • written 3 months ago by • 0
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1
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273
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
2
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2
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691
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Handling biological replicates in DESeq2
DESeq2
updated 3 months ago by ★ 4.7k • written 3 months 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 20 days ago by • 0 • written 6.1 years ago by ▴ 30
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6
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1.1k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 3 months ago by 43k • written 3 months ago by ▴ 10
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2
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423
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 3 months ago by • 0
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5
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750
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
3 months ago LuciaNhu • 0
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1
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458
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Average expression of genes across replicates
DESeq2
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
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0
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181
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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 Denise • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: SingleR with multiple single cell references by Aaron Lun ★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies by ATpoint ★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2? by ATpoint ★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2? by Wolfgang Huber ★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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