Showing : DeSeq2 • reset
2
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4
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206
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Differential variability modelling with vst() expression
limma DESeq2
updated 3 days ago by 43k • written 4 days ago by • 0
0
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2
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251
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
4 days ago • updated 2 days ago sindhuri • 0
2
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8
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532
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
5 days ago • updated 3 days ago Quang ▴ 10
1
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1
reply
250
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 6 days ago by 43k • written 6 days ago by • 0
0
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1
reply
121
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 7 days ago by ★ 1.4k • written 7 days ago by • 0
0
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1
reply
320
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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 10 days ago by 43k • written 20 days ago by • 0
2
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1
reply
327
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 10 days ago by 43k • written 17 days ago by • 0
0
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2
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236
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
15 days ago • updated 14 days ago Kucsera • 0
1
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1
reply
351
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 24 days ago by 43k • written 4 weeks ago by • 0
1
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9
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761
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 27 days ago by ▴ 30
0
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2
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284
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 27 days ago by ★ 4.6k • written 4 weeks ago by • 0
1
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5
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519
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Deseq2 Design
RNASeq DESeq2
updated 28 days ago by 67k • written 4 weeks ago by • 0
0
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5
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483
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p value is 0, padj is 0
DESeq2
4 weeks ago Wirayatida • 0
1
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2
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470
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
4 weeks ago georgii.vdovin • 0
0
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7
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770
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 4 weeks ago by • 0 • written 5 weeks ago by • 0
0
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1
reply
262
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 5 weeks ago by 43k • written 5 weeks ago by ▴ 20
0
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3
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401
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DESeq2 - Comparing Comparisons
DESeq2
updated 4 weeks ago by 67k • written 5 weeks ago by • 0
0
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4
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522
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lfcShrink and alpha value
lfcShrink DESeq2
6 weeks ago • updated 5 weeks ago cropero • 0
1
vote
1
reply
268
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 5 weeks ago by 43k • written 7 weeks ago by • 0
0
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2
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203
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 5 weeks ago by 43k • written 6 weeks ago by • 0
0
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2
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259
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
6 weeks ago Anna • 0
1
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2
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548
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Deseq2 res Function
DESeq2
updated 7 weeks ago by 67k • written 7 weeks ago by ▴ 10
0
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4
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419
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
7 weeks ago NB • 0
0
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5
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435
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Identical samples after deseq2 batch effect removal
DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
0
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1
reply
241
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 7 weeks ago by 67k • written 7 weeks ago by • 0
1
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2
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304
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
7 weeks ago Denise • 0
0
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1
reply
161
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eRNAs count
RNASeq DESeq2
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
0
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1
reply
400
views
DESeq2 rerun returns different results
DESeq2
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
0
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1
reply
249
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
0
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1
reply
235
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 8 weeks ago by ★ 4.1k • written 8 weeks ago by • 0
2
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2
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629
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Handling biological replicates in DESeq2
DESeq2
updated 8 weeks ago by ★ 4.6k • written 9 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
1
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6
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997
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 9 weeks ago by 43k • written 9 weeks ago by ▴ 10
0
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2
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386
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 9 weeks ago by • 0
4
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5
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672
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
9 weeks ago LuciaNhu • 0
0
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1
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409
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Average expression of genes across replicates
DESeq2
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
0
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0
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146
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
10 weeks ago info ▴ 10
0
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10
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1.3k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
10 weeks ago • updated 9 weeks ago Denise • 0
0
votes
1
reply
360
views
Deseq to output continous sequencing data
DESeq2
updated 11 weeks ago by 43k • written 3 months ago by • 0
1
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4
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855
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Adjusted p-values become NA when sub-setting samples
DESeq2
3 months ago • updated 9 weeks ago txema.heredia • 0
3
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3
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935
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 11 weeks ago by • 0
0
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2
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372
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 11 weeks ago by • 0
0
votes
1
reply
312
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 11 weeks ago by 43k • written 11 weeks ago by • 0
2
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3
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1.0k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
1
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4
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786
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DESeq2 - interactions when using factors concatenated into group
DESeq2
12 weeks ago • updated 11 weeks ago boczniak767 ▴ 740
0
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1
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221
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
12 weeks ago JY • 0
0
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1
reply
300
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
0
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2
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234
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how to extract expression matrix post deseq2
DESeq2
written 12 weeks ago by • 0
0
votes
2
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229
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Using Normalized Counts in DESeq2
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
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2
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288
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When running contrasts, does it use normalized read counts?
DESeq2
3 months ago Katherine • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
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