Showing : Deseq2 • reset
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
updated 14 hours ago by 42k • written 1 day ago by • 0
4
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5
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459
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
2 days ago • updated 1 day ago LuciaNhu • 0
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1
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299
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Average expression of genes across replicates
DESeq2
updated 4 days ago by ★ 4.5k • written 5 days ago by • 0
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68
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
7 days ago info ▴ 10
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10
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1.1k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
8 days ago • updated 1 day ago Denise • 0
0
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1
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281
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Deseq to output continous sequencing data
DESeq2
updated 9 days ago by 42k • written 26 days ago by • 0
1
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4
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596
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Adjusted p-values become NA when sub-setting samples
DESeq2
27 days ago • updated 12 hours ago txema.heredia • 0
3
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2
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642
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
updated 10 days ago by ★ 4.5k • written 11 days ago by • 0
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1
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172
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
updated 13 days ago by 42k • written 15 days ago by • 0
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1
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233
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 16 days ago by 42k • written 16 days ago by • 0
2
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3
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929
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Analysis of large RNA-Seq Datasets
DESeq2
updated 18 days ago by 42k • written 19 days ago by • 0
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4
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673
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DESeq2 - interactions when using factors concatenated into group
DESeq2
20 days ago • updated 12 days ago boczniak767 ▴ 740
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1
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158
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
21 days ago • updated 20 days ago JY • 0
0
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1
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237
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
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2
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167
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how to extract expression matrix post deseq2
DESeq2
written 21 days ago by • 0
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2
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157
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Using Normalized Counts in DESeq2
DESeq2
updated 22 days ago by 42k • written 22 days ago by • 0
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2
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198
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When running contrasts, does it use normalized read counts?
DESeq2
23 days ago Katherine • 0
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1
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166
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 24 days ago by ★ 1.4k • written 26 days ago by • 0
3
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4
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412
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
26 days ago Eva ▴ 10
1
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4
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428
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 22 days ago by ★ 4.5k • written 4 weeks ago by • 0
0
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1
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143
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 28 days ago by 42k • written 29 days ago by • 0
3
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11
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635
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 4 weeks ago by • 0
2
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4
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341
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
29 days ago jihoon.kim.1495 ▴ 10
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6
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722
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 11 days ago by 42k • written 4 weeks ago by • 0
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4
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387
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 4 weeks ago by ★ 4.5k • written 5 weeks ago by • 0
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2
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241
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
4 weeks ago paul.meraner • 0
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156
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
4 weeks ago • updated 7 days ago info ▴ 10
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5
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462
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heatmap with batch effect
DESeq2 BatchEffect
4 weeks ago tothuhien • 0
0
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2
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319
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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 5 weeks ago by 42k • written 5 weeks ago by • 0
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1
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217
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
1
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1
reply
210
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 5 weeks ago by ★ 4.5k • written 5 weeks ago by • 0
1
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1
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295
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 5 weeks ago by ★ 4.5k • written 5 weeks ago by • 0
1
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2
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405
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 10
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2
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664
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
1
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2
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454
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 5 weeks ago by 42k • written 7 weeks ago by ▴ 10
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6
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645
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 19 days ago by ★ 4.5k • written 6 weeks ago by • 0
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1
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267
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
17
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9
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6.9k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7 weeks ago by 67k • written 8.4 years ago by ▴ 10
0
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1
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257
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
0
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2
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474
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 8 weeks ago by ★ 1.4k • written 9 weeks ago by • 0
0
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5
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1.6k
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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 8 weeks ago by 42k • written 8 weeks ago by • 0
3
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6
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27k
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Deseq: What does "BaseMean" mean?
deseq2
written 6.1 years ago by • 0
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2
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827
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 9 weeks ago by ★ 1.4k • written 9 weeks ago by • 0
4
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11
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736
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
10 weeks ago • updated 9 weeks ago boczniak767 ▴ 740
3
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4
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401
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Gene filtering in DESeq2
DESeq2
updated 10 weeks ago by ★ 4.5k • written 10 weeks ago by • 0
0
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2
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394
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 10 weeks ago by • 0
1
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2
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274
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Deseq2 - differenc in results
DESeq2
written 10 weeks ago by • 0
0
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7
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585
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DESeq design with and without intercept is giving different results
DESeq2
written 10 weeks ago by • 0
1
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5
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733
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 10 weeks ago by 51k • written 10 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open! by Esperan • 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
Votes
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
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