Showing : DESEQ2 • reset
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
2 days ago • updated 1 day ago Marwan • 0
1
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2
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971
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 6 days ago by ★ 4.7k • written 7 days ago by • 0
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1
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125
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 9 days ago by 43k • written 14 days ago by • 0
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3
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442
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 10 days ago by • 0 • written 15 days ago by • 0
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2
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335
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 13 days ago by • 0 • written 18 days ago by • 0
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2
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303
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
18 days ago • updated 17 days ago Martijn • 0
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3
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346
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 18 days ago by • 0 • written 26 days ago by ▴ 10
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1
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155
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 22 days ago by 43k • written 23 days ago by • 0
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2
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426
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 24 days ago by ★ 1.4k • written 28 days ago by • 0
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4
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928
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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
26 days ago • updated 23 days ago Quang NN ▴ 10
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2
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363
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
29 days ago • updated 27 days ago Blandine • 0
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5
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319
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 4 weeks ago by • 0
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4
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455
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
4 weeks ago Quang NN ▴ 10
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5
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369
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Differential variability modelling with vst() expression
limma DESeq2
written 6 weeks ago by • 0
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3
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515
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 6 weeks ago by • 0
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9
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902
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
6 weeks ago • updated 4 weeks ago Quang NN ▴ 10
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1
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358
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 6 weeks ago by 43k • written 6 weeks ago by • 0
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1
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198
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 6 weeks ago by ★ 1.4k • written 6 weeks ago by • 0
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1
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378
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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 8 weeks ago by • 0
2
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1
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374
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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 8 weeks ago by • 0
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2
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336
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
7 weeks ago Kucsera • 0
1
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1
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394
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 8 weeks ago by 43k • written 10 weeks ago by • 0
1
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9
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880
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 9 weeks ago by ▴ 30
4
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2
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443
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 9 weeks ago by ★ 4.7k • written 10 weeks ago by ▴ 10
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5
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614
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Deseq2 Design
RNASeq DESeq2
updated 9 weeks ago by 68k • written 10 weeks ago by • 0
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5
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579
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p value is 0, padj is 0
DESeq2
10 weeks ago Wirayatida • 0
1
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2
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562
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
10 weeks ago georgii.vdovin • 0
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7
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893
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 10 weeks ago by • 0 • written 10 weeks ago by • 0
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1
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320
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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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456
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DESeq2 - Comparing Comparisons
DESeq2
updated 10 weeks ago by 68k • written 11 weeks ago by • 0
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4
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589
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lfcShrink and alpha value
lfcShrink DESeq2
11 weeks ago cropero • 0
2
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1
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344
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 11 weeks ago by 43k • written 12 weeks ago by • 0
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250
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 11 weeks ago by 43k • written 11 weeks ago by • 0
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293
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
12 weeks ago Anna • 0
1
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2
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590
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Deseq2 res Function
DESeq2
updated 12 weeks ago by 68k • written 12 weeks ago by ▴ 10
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4
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482
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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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508
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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
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285
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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
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348
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
3 months ago Denise • 0
0
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1
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197
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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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444
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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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300
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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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282
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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
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2
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698
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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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26k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 25 days ago by • 0 • written 6.1 years ago by ▴ 30
1
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6
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1.1k
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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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428
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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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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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464
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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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184
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
3 months ago info ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data by user_bioinfo • 0
yes actually that's why I did, and its all good! thank you for your response
Comment: batch effect removal for agilent microarray data by gaye.yilmaz • 0
Hello again, Can using inSilicoMerging handle this situation?
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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