Showing : DEseq2 • reset
4
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1.2k
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 13 months ago by ★ 5.0k • written 13 months ago by ▴ 10
1
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5
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1.2k
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Deseq2 Design
RNASeq DESeq2
updated 13 months ago by 68k • written 13 months ago by • 0
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5
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1.3k
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p value is 0, padj is 0
DESeq2
13 months ago Wirayatida • 0
1
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2
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1.3k
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
13 months ago georgii.vdovin • 0
0
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7
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1.4k
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 13 months ago by • 0 • written 13 months ago by • 0
0
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1
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595
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 13 months ago by 43k • written 13 months ago by ▴ 20
0
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3
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827
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DESeq2 - Comparing Comparisons
DESeq2
updated 13 months ago by 68k • written 13 months ago by • 0
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4
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1.0k
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lfcShrink and alpha value
lfcShrink DESeq2
14 months ago • updated 13 months ago anon • 0
2
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1
reply
833
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 13 months ago by 43k • written 14 months ago by • 0
0
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2
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542
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
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2
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533
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
14 months ago Anna • 0
1
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2
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849
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Deseq2 res Function
DESeq2
updated 14 months ago by 68k • written 14 months ago by ▴ 10
0
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4
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815
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
14 months ago NB • 0
0
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5
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808
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Identical samples after deseq2 batch effect removal
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
0
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1
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627
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 14 months ago by 68k • written 14 months ago by • 0
1
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2
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532
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
14 months ago Denise • 0
0
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1
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472
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eRNAs count
RNASeq DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
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1
reply
659
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DESeq2 rerun returns different results
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
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1
reply
570
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 14 months ago by 43k • written 14 months ago by • 0
0
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1
reply
698
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
2
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2
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1.2k
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Handling biological replicates in DESeq2
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
5
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3
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29k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 7.0 years ago by ▴ 30
1
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6
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1.7k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 14 months ago by 43k • written 14 months ago by ▴ 10
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2
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600
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 14 months ago by • 0
4
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5
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1.5k
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
14 months ago LuciaNhu • 0
0
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1
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793
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Average expression of genes across replicates
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
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0
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466
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
15 months ago info ▴ 10
0
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11
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2.6k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 9 months ago by • 0 • written 15 months ago by • 0
0
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1
reply
586
views
Deseq to output continous sequencing data
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
1
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4
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1.5k
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Adjusted p-values become NA when sub-setting samples
DESeq2
15 months ago • updated 14 months ago txema.heredia • 0
3
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3
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1.7k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 15 months ago by • 0
0
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2
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968
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 15 months ago by • 0
0
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1
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514
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
2
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3
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1.3k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
1
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4
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1.2k
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DESeq2 - interactions when using factors concatenated into group
DESeq2
15 months ago boczniak767 ▴ 740
0
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1
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411
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
15 months ago JY • 0
0
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1
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499
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
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2
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538
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how to extract expression matrix post deseq2
DESeq2
written 15 months ago by • 0
0
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2
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573
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Using Normalized Counts in DESeq2
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
3
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2
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675
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When running contrasts, does it use normalized read counts?
DESeq2
15 months ago Katherine ▴ 20
0
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1
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449
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
3
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4
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1.5k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
15 months ago Eva ▴ 10
1
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4
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1.4k
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
0
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1
reply
565
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
2
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4
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1.0k
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
15 months ago jihoon.kim.1495 ▴ 10
0
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6
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1.5k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 15 months ago by 43k • written 15 months ago by • 0
5
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4
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1.1k
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
0
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2
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757
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
15 months ago paul.meraner • 0
0
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0
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665
views
News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
15 months ago info ▴ 10
1
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6
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1.6k
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heatmap with batch effect
DESeq2 BatchEffect
written 15 months ago by • 0
4,845 results • Page 3 of 97
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This rotation style program sounds like a great way to explore different fields before committing to one. Similarly, apkgamex lets users ex…
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This compliance focused approach makes a lot of sense. Clear reminders and opt in policies help maintain trust, similar to how users look f…
Comment: Bile acid analysis with limpa by ATpoint ★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
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I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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