Showing : desEQ2 • reset
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27
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
10 hours ago Luca • 0
0
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1
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150
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 1 day ago by ★ 4.7k • written 2 days ago by ▴ 20
4
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4
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772
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
6 days ago • updated 4 days ago Elijah • 0
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1
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146
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 5 days ago by 43k • written 6 days ago by • 0
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3
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575
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how many significant figures are there in DESeq2 output
DESeq2
updated 9 days ago by ★ 4.7k • written 11 days ago by ▴ 180
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5
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963
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
13 days ago • updated 12 days ago picasa1983 • 0
3
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7
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2.0k
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 12 days ago by ▴ 10 • written 6.0 years ago by ▴ 20
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1
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299
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How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 14 days ago by 68k • written 14 days ago by • 0
1
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1
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427
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 15 days ago by ★ 1.4k • written 15 days ago by ▴ 10
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1
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267
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DEseq2 design for additive treatment
DESeq2
updated 15 days ago by ★ 4.7k • written 16 days ago by • 0
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2
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474
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Plot title for PCA in DESeq2
DESeq2
17 days ago • updated 14 days ago AL • 0
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3
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528
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 18 days ago by 43k • written 21 days ago by • 0
1
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2
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1.0k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 25 days ago by ★ 4.7k • written 25 days ago by • 0
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1
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146
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 28 days ago by 43k • written 4 weeks ago by • 0
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3
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499
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 28 days ago by • 0 • written 4 weeks ago by • 0
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2
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367
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 4 weeks ago by • 0 • written 5 weeks ago by • 0
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3
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434
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 14 days ago by • 0 • written 5 weeks ago by • 0
0
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3
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391
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 5 weeks ago by • 0 • written 6 weeks ago by ▴ 10
0
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1
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206
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 5 weeks ago by 43k • written 6 weeks ago by • 0
2
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2
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460
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 6 weeks ago by ★ 1.4k • written 6 weeks ago by • 0
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4
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965
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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 weeks ago Quang NN ▴ 10
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2
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472
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
6 weeks ago Blandine • 0
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5
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348
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 7 weeks ago by • 0
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4
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498
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
7 weeks ago • updated 6 weeks ago Quang NN ▴ 10
2
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5
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402
views
Differential variability modelling with vst() expression
limma DESeq2
written 8 weeks ago by • 0
0
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3
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555
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 8 weeks ago by • 0
2
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9
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990
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
8 weeks ago • updated 7 weeks ago Quang NN ▴ 10
1
vote
1
reply
424
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
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1
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210
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 9 weeks ago by ★ 1.4k • written 9 weeks ago by • 0
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1
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400
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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 9 weeks ago by 43k • written 11 weeks ago by • 0
2
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1
reply
402
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
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2
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391
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
10 weeks ago Kucsera • 0
1
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1
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411
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 11 weeks ago by 43k • written 3 months ago by • 0
1
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9
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924
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 12 weeks ago by ▴ 30
4
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2
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495
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 12 weeks ago by ★ 4.7k • written 12 weeks ago by ▴ 10
1
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5
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643
views
Deseq2 Design
RNASeq DESeq2
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
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5
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643
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p value is 0, padj is 0
DESeq2
12 weeks ago Wirayatida • 0
1
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2
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622
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
3 months ago • updated 12 weeks ago georgii.vdovin • 0
0
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7
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963
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 3 months ago by • 0 • written 3 months ago by • 0
0
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1
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357
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 3 months ago by 43k • written 3 months ago by ▴ 20
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3
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498
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DESeq2 - Comparing Comparisons
DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
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4
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634
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lfcShrink and alpha value
lfcShrink DESeq2
3 months ago cropero • 0
2
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1
reply
394
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 3 months ago by 43k • written 3 months ago by • 0
0
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2
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281
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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2
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315
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
3 months ago Anna • 0
1
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2
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624
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Deseq2 res Function
DESeq2
updated 3 months ago by 68k • written 3 months ago by ▴ 10
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4
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512
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
3 months ago NB • 0
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5
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551
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Identical samples after deseq2 batch effect removal
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
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1
reply
305
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
1
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2
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371
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
3 months ago Denise • 0
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Comment: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf by AB ▴ 110
Force=TRUE did the trick. Thank you.
Comment: www.stats.ox.ac.uk seems to be off, leading to errors/delays when installing pac by DENG • 0
[https://github.com/djunsheep/CRANextra/blob/main/README.md][1] add the following to the `.Rprofile` and `Rprofile.site` # fixing the…
Comment: Transcript ID Mismatch in riboWaltz Annotation Table by shepherl 4.1k
riboWalze is not a Bioconductor package and does not appear to be a Bioconductor function; the maintainer is not guaranteed to be on this …
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf by shepherl 4.1k
What is your `sessionInfo()`? I just tried locally and it works fine so there might have been a bad or interrupted download when initially…
Comment: error in ChAMP loading file by shocked.tick.zyet • 0
Great troubleshooting steps for ChAMP import issues! "ChAMP methylation data import errors" on [Google Search][1] for similar cases. Header…
Votes
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
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