Showing : DESeq2 • reset
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
updated 11 hours ago by 67k • written 15 hours ago by • 0
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1
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71
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eRNAs count
RNASeq DESeq2
updated 2 days ago by ★ 4.5k • written 2 days ago by • 0
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1
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335
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DESeq2 rerun returns different results
DESeq2
updated 5 days ago by ★ 4.5k • written 6 days ago by • 0
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1
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166
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 6 days ago by 42k • written 7 days ago by • 0
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1
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132
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 8 days ago by ★ 4.1k • written 8 days ago by • 0
2
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2
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516
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Handling biological replicates in DESeq2
DESeq2
updated 8 days ago by ★ 4.5k • written 9 days ago by • 0
5
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2
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25k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
1
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6
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858
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 12 days ago by 42k • written 12 days ago by ▴ 10
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2
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317
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 14 days ago by • 0
4
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5
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561
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
16 days ago • updated 15 days ago LuciaNhu • 0
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1
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353
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Average expression of genes across replicates
DESeq2
updated 18 days ago by ★ 4.5k • written 19 days ago by • 0
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101
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
21 days ago info ▴ 10
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10
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1.2k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
22 days ago • updated 15 days ago Denise • 0
0
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1
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308
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Deseq to output continous sequencing data
DESeq2
updated 23 days ago by 42k • written 5 weeks ago by • 0
1
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4
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732
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Adjusted p-values become NA when sub-setting samples
DESeq2
5 weeks ago • updated 14 days ago txema.heredia • 0
3
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3
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825
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 25 days ago by • 0
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2
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311
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 29 days ago by • 0
0
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1
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264
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
2
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3
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983
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Analysis of large RNA-Seq Datasets
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
1
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4
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716
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DESeq2 - interactions when using factors concatenated into group
DESeq2
4 weeks ago • updated 26 days ago boczniak767 ▴ 740
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1
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180
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
4 weeks ago JY • 0
0
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1
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258
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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2
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186
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how to extract expression matrix post deseq2
DESeq2
written 5 weeks ago by • 0
0
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2
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181
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Using Normalized Counts in DESeq2
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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2
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226
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When running contrasts, does it use normalized read counts?
DESeq2
5 weeks ago Katherine • 0
0
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1
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182
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 5 weeks ago by ★ 1.4k • written 5 weeks ago by • 0
3
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4
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453
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
5 weeks ago Eva ▴ 10
1
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4
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461
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 5 weeks ago by ★ 4.5k • written 6 weeks ago by • 0
0
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1
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165
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
3
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11
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695
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 6 weeks ago by • 0
2
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4
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383
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
6 weeks ago jihoon.kim.1495 ▴ 10
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6
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782
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 25 days ago by 42k • written 6 weeks ago by • 0
5
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4
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422
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 6 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
0
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2
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263
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
6 weeks ago paul.meraner • 0
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0
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174
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
6 weeks ago • updated 21 days ago info ▴ 10
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5
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536
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heatmap with batch effect
DESeq2 BatchEffect
6 weeks ago tothuhien • 0
0
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2
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341
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
1
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1
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249
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 7 weeks ago by 67k • written 7 weeks ago by • 0
1
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1
reply
225
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 7 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
1
vote
1
reply
315
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 7 weeks ago by ★ 4.5k • written 7 weeks ago by • 0
1
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2
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432
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 7 weeks ago by 42k • written 8 weeks ago by ▴ 10
0
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2
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686
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 7 weeks ago by 42k • written 8 weeks ago by • 0
1
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2
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485
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 7 weeks ago by 42k • written 9 weeks ago by ▴ 10
1
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6
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685
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 4 weeks ago by ★ 4.5k • written 8 weeks ago by • 0
0
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1
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286
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
17
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9
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7.0k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 9 weeks ago by 67k • written 8.5 years ago by ▴ 10
0
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1
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277
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
0
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2
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496
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 10 weeks ago by ★ 1.4k • written 11 weeks ago by • 0
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5
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1.7k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.5 years ago by • 0
3
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6
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1.4k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 10 weeks ago by 42k • written 10 weeks ago by • 0
50 results • Page 1 of 1
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Answer: Unlocking Potential: NURS FPX Strategies and Insights by efsane_kral2000 • 0
https://diendannhansu.com/threads/hayal-sohbet-odalari.667004/ https://forum.realdigital.org/u/serkan https://animefagos.com/miembros/ser…
Comment: Unlocking Potential: NURS FPX Strategies and Insights by efsane_kral2000 • 0
https://www.hayalsohbet.net https://www.yerlichat.com https://www.yerlichat.net https://www.mavisim.net https://www.hayalchat.com http…
Comment: Is it recommended to analyze different tissues together when using edgeR by Gordon Smyth 51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
Comment: Handling Epic Array Data by Melisa Tecik • 0
Thanks a lot for the help. You saved my day
Answer: Differene between the Wald and LRT test for time-series gene expression data by James W. MacDonald 67k
The advantage to using the LRT is that it's an omnibus test that tells you if there are changes at any time point. If you have lots of time…
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Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Answer: Allele frequencies for ALL alleles of one SNP ?
Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Using Affymetrix Custom Array
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